4_1_Jan_SF_Bin18_scaffold_700_c1_6270-9776_1

SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "4_1_Jan_SF_Bin18_scaffold_700_c1_6270-9776_1" submitted to SWISS-MODEL workspace on March 29, 2023, 8:51 p.m..The submitted primary amino acid sequence is given in Table T1.

If you use any results in your research, please cite the relevant publications:

Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 (2018).
Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319 (2017).
Studer, G., Tauriello, G., Bienert, S., Biasini, M., Johner, N., Schwede, T. ProMod3 - A versatile homology modelling toolbox. PLOS Comp. Biol. 17(1), e1008667 (2021).
Studer, G., Rempfer, C., Waterhouse, A.M., Gumienny, G., Haas, J., Schwede, T. QMEANDisCo - distance constraints applied on model quality estimation. Bioinformatics 36, 1765-1771 (2020).
Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., Schwede, T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports 7 (2017).

Results

The SWISS-MODEL template library (SMTL version 2023-03-23, PDB release 2023-03-17) was searched with for evolutionary related structures matching the target sequence in Table T1. For details on the template search, see Materials and Methods. Overall 513 templates were found (Table T2).

Models

The following models were built (see Materials and Methods "Model Building"):

Model #01	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	1 x MO: MOLYBDENUM ATOM;	0.70	0.71 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
7b04.1.B	40.77	monomer	0.00	BLAST	X-ray	2.97Å	0.41	28 - 1160	0.96	Nitrite oxidoreductase subunit A

Included Ligands

Ligand	Description
1 x MO	MOLYBDENUM ATOM

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
CA.10	Binding site not conserved.	CALCIUM ION
CA.11	Binding site not conserved.	CALCIUM ION
F3S.4	Binding site not conserved.	FE3-S4 CLUSTER
HEM.9	Binding site not conserved.	PROTOPORPHYRIN IX CONTAINING FE
MD1.5	Binding site not conserved.	PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MD1.6	Binding site not conserved.	PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
SF4.1	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.2	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.3	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.8	Binding site not conserved.	IRON/SULFUR CLUSTER

Target    SDLSRRELLKRAVVVGTGAGLAELFLPAQFLSSASAQSEPQAVAIANPLAQMPDRSWERIYRDQFAEEDSFVFTCAPNDT
7b04.1.B  --LTRRAFLQVAGATGATLTLAKNAMAFRLLKPA--------VVVDNPLDTYPDRRWESVYRDQYQYDRTFTYCCSPNDT

Target    HNCLLRAHVKNGVIVRISPTYGYGKATDLAGNQASHRWDPRICQKGLILGRRIYGDRRVKAPMIRKGFKEWADAGFPRHD
7b04.1.B  HACRIRAFVRNNVMMRVEQNYDHQNYSDLYGNKATRNWNPRMCLKGYTFHRRVYGPYRLRYPLIRKGWKRWADDGFPELT

Target    -DGTPRADMEKRGYDEWLQIPWDEALAIAAKTLQNVAETYKGEDGAGKLLEQGYEPAMVEAMHGAGVQAIKMRGGMPLLG
7b04.1.B  PENKTKYMFDNRGNDELLRASWDEAFTYASKGIIHITKKYSGPEGAQKLIDQGYPKEMVDRMQGAGTRTFKGRGGMGLLG

Target    AGRVFGFYRFANMLALLDGKLRPEAPPEEIVGSRAFDNYAWHTDLPPGHPMVSGSQTVDFDLFAAEHSKLLVLIGMNWIC
7b04.1.B  VIGKYGMYRFNNCLAIVDAHNRGVGP-DQALGGRNWSNYTWHGDQAPGHPFSHGLQTSDVDMNDVRFSKLLIQTGKNLIE

Target    TKMPDAHWIGDARLKGTRVVVISADYMPTANKADEIVILRPGTDTAFLLGVARELITKKLYDRDAVIQRTDLPLLVRLDT
7b04.1.B  NKMPEAHWVTEVMERGGKIVVITPEYSPSAQKADYWIPIRNNTDTALFLGITKILIDNKWYDADYVKKFTDFPLLIRTDT

Target    GERLSARDVFEGYRQAPLENYVALKTEEELAAPPSPPFTADKQVVPTELREEWGDFVYWDRATNGPAAVNRDEIG---AK
7b04.1.B  LKRVSPKDIIPNYKL------------QDISDGPSYHI----QGLKDEQREIIGDFVVWDAKSKGPKAITRDDVGETLVK

Target    FAGDPALLGAFDVTLVDGTNVKARTAFSLLKEYLDENFDVQTTSEVCNVDPAAVRSLARQLAANKGNALLAAGMGPNHYF
7b04.1.B  KGIDPVLEGSFKLKTIDGKEIEVMTLLEMYKIHL-RDYDIDSVVSMTNSPKDLIERLAKDIATIKPVAIHYGE-GVNHYF

Target    NADLFGRVHFLVAALTDNIGHFSGNVGSYAGNYRGSLFQA-------MGQWIAENPFDQEADLTKPAR---VKRYFKSES
7b04.1.B  HATLMNRSYYLPVMLTGNVGYFGSGSHTWAGNYKAGNFQASKWSGPGFYGWVAEDVFKPNLDPYASAKDLNIKGRALDEE

Target    AHYWNYGDRPLVSPS-----EIITGKSHMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPKQDAVFCNEWHWTSSCEYSD
7b04.1.B  VAYWNHSERPLIVNTPKYGRKVFTGKTHMPSPTKVLWFTNVN-LINNAKHVYQMLKNVNPNIEQIMSTDIEITGSIEYAD

Target    LVFPADSWAEFKLPDMTASCTNPFLLAFPKTPLARIHNTRSDYEILAGVAAALADLVDEPRMKTYWKGILDGDPTPYLQR
7b04.1.B  FAFPANSWVEFQEFEITNSCSNPFIQIWGKTGITPVYESKDDVKILAGMASKLGELLRDKRFEDNWKFAIEGRASVYINR

Target    VLSGSNATRGILYEDLHASS--AKGVPLLMNARTYPRHAGWEQRQEDKPWYTPTGRLEFYRPEPEWQAAGESLPIWREPV
7b04.1.B  LLDGSTTMKGYTCEDILNGKYGEPGVAMLL-FRTYPRHPFWEQVHESLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGP

Target    DATFYEPNAILANSKHPSINPRAPEDYGVPESQMDVETRQYRNVVRTWQELKLSKHPLTEKDPAYRFVFQTPKYRWGAHS
7b04.1.B  EATPYLPNAIV--STNPYIR---PDDYGIPENAEYWEDRTVRNIKKSWEETKKTKNFLWEK--GYHFYCVTPKSRHTVHS

Target    TAVDSDWIAMLFGPFGDPYRRDSRTPWTGEAYAEINPRDAKELGLKDGDYIWLDADPEDRPYRGADSSDEFYDVARAMMR
7b04.1.B  QWAVTDWNFIWNNNFGDPYRMDKRMPGVGEHQIHIHPQAARDLGIEDGDYVYVDANPADRPYEGWKPNDSFYKVSRLMLR

Target    VRIYSGMPRRVIRTWFNMYAATPGTVQAQKDVPGGPAQNQDTGYVALFRHGSHQSGTRAYLRPTQMTDSMNRKAYFGQTI
7b04.1.B  AKYNPAYPYNCTMMKHSAWISSDKTVQAHETRPDGRALSP-SGYQSSFRYGSQQSITRDWSMPMHQLDSLFHKAKIGMKF

Target    GKGFEADVHSPSGAPKEGYVKVEKAEDGGDEGVGEWRPVTLGLRPDDPSEAMQAYLAGEFVTRKRKGS
7b04.1.B  IFGFEADNHCINTVPKETLVKITKAENGGMGGKGVWDPVKTGYTAGNENDFMKKFLNGELI-------

Model #02	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.41	0.51 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
3ir5.1.A	24.12	monomer	0.00	HHblits	X-ray	2.30Å	0.32	54 - 1130	0.78	Respiratory nitrate reductase 1 alpha chain

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
6MO.3	Clashing with protein.	MOLYBDENUM(VI) ION
AGA.5	Binding site not conserved.	(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
F3S.9	Binding site not conserved.	FE3-S4 CLUSTER
HEM.10	Binding site not conserved.	PROTOPORPHYRIN IX CONTAINING FE
HEM.11	Binding site not conserved.	PROTOPORPHYRIN IX CONTAINING FE
MD1.1	Binding site not conserved.	PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MD1.2	Binding site not conserved.	PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
SF4.4	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.6	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.7	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.8	Binding site not conserved.	IRON/SULFUR CLUSTER

Target    SDLSRRELLKRAVVVGTGAGLAELFLPAQFLSSASAQSEPQAVAIANPLAQMPDRSWERIYRDQFAEEDSFVFTCAPNDT
3ir5.1.A  -----------------------------------------------------NRDWEDGYRQRWQHDKIVRSTCGVNCT

Target    HNCLLRAHVKNGVIVRISPTYGYGKATDLAGNQASHRWDPRICQKGLILGRRIYGDRRVKAPMIRKGFKE-WADAGFP--
3ir5.1.A  GSCSWKIYVKNGLVTWETQQTDYPR-----TRPDLPNHEPRGCPRGASYSWYLYSANRLKYPMMRKRLMKMWREAKALHS

Target    -------R-HD-DGTPRADMEKRGYDEWLQIPWDEALAIAAKTLQNVAETYKGEDGAGKLLEQGYEPAMVEAMHGAGVQA
3ir5.1.A  DPVEAWASIIEDADKAKSFKQARGRGGFVRSSWQEVNELIAASNVYTIKNYGPDR----VAG----------FSPIPAMS

Target    IKMRGGMPLLGAGRVFGFYRFANMLALLDGKLRPEAPPEEIVGSRAFDNYAWHTDLPPGHPMVSGSQTVDFDLFAAEHSK
3ir5.1.A  M-----------VSYASGARYLS-----------------LIGGTCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSS

Target    LLVLIGMNWICTKMPDAHWIGDARLKGTRVVVISADYMPTANKADEIVILRPGTDTAFLLGVARELITKKL------YDR
3ir5.1.A  YIIAWGSNVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFT

Target    DAVIQRTDLPLLVRLD-------TGERLSARDVFEGYRQAPL--ENYVALKTEEELAAPPSPPFTADKQVVPT-ELREEW
3ir5.1.A  DYVRRYTDMPMLVMLEERDGYYAAGRMLRAADLVDALGQENNPEWKTVAFNT-------------NGEMVAPNGSIGFRW

Target    GDFVYWDR-----ATNGPAAVNR------DE----IGAKFA-----------GDPALLG---AFDVTLVDGTNVKARTAF
3ir5.1.A  GEKGKWNLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVY

Target    SLLK------------------EYLDENFDVQTTSEVCNVDPAAVRSLARQLAANK----GNALLAAGMGPNHYFNADLF
3ir5.1.A  DLTLANYGLERGLNDVNCATSYDDV-KAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHLDMN

Target    GRVHFLVAALTDNIGHFSGNVGSYAGNYRGSLFQAMGQ--------------------------WIAENPFDQEADLTKP
3ir5.1.A  YRGLINMLIFCGCVGQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEE--LLSP

Target    A-RVKRYFK--------SESAHYW----NYGDRPL----------V-----SPSEIITGKS--------HMPTPTKLIWF
3ir5.1.A  MADKSRYTGHLIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLFI

Target    GNSNSLLGNAKWSFDV------------------------------VKNTLPKQDAVFCNEWHWTSSCEYSDLVFPADSW
3ir5.1.A  WRSNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATW

Target    AEFKLPDMTASCTNPFLLAFPKTPLARIHNTRSDYEILAGVAAALADLVDEP------------------------RMKT
3ir5.1.A  YEK--DDMNTSDMHPFIHPLSA-AVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPIQHDSAAELAQPLDVKD

Target    YWKGILD---G------------------------------------------DPTPYLQ--------------------
3ir5.1.A  WKKGECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTA

Target    -----RVLSGSNATRGI----LYEDLHASSA-----------KGVPLLMNA------------------RTYPRHAGWEQ
3ir5.1.A  IDAAEMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYTN

Target    RQEDKPWYTPTGRLEFYRPEPEWQAAGESLPIWREPVDATFYEPNAILANSKHPSINPRAPEDYGVPESQMDVETRQYRN
3ir5.1.A  VHELIPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSVKE-------------------V----------------

Target    VVRTWQELKLSKHPLTEKDPAYRFVFQTPKYRWGAHSTAVDSDWIAMLFGPFGDPYRRDSRTPWTGEAYAEINPRDAKEL
3ir5.1.A  -----I------GQKSNGNQEKALNFLTPHQKWGIHSTYSDNLLMLTLG---------------RGGPVVWLSEADAKDL

Target    GLKDGDYIWLDADPEDRPYRGADSSDEFYDVARAMMRVRIYSGMPRRVIRTWFNMYAATPGTVQAQKDVPGGPAQNQDTG
3ir5.1.A  GIADNDWIEVFNS-----------------NGALTARAVVSQRVPAGMTMMYHAQERIVN--------LPGSEI------

Target    YVALFRHGSHQSGTRAYLRPTQMTDSMNRKAYFGQTIGKGFEADVHSPSGAPKEGYVKVEKAEDGGDEGVGEWRPVTLGL
3ir5.1.A  --TQQRGGIHNSVTRITPKPTHMIGGYAHLAY-------G--FNYYGTVGSNRDEFVVVRKMKNIDWL------------

Target    RPDDPSEAMQAYLAGEFVTRKRKGS
3ir5.1.A  -------------------------

Model #03	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.27	0.47 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
1h0h.1.A	17.09	monomer	0.00	HHblits	X-ray	1.80Å	0.28	69 - 756	0.47	FORMATE DEHYDROGENASE SUBUNIT ALPHA

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
2MD.2	Binding site not conserved.	GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER
CA.6	Binding site not conserved.	CALCIUM ION
EPE.7	Not biologically relevant.	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
MGD.3	Binding site not conserved.	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
SF4.5	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.8	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.9	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.10	Binding site not conserved.	IRON/SULFUR CLUSTER
UNX.4	Not biologically relevant.	UNKNOWN ATOM OR ION
W.1	Not in contact with model.	TUNGSTEN ION

Target    SDLSRRELLKRAVVVGTGAGLAELFLPAQFLSSASAQSEPQAVAIANPLAQMPDRSWERIYRDQFAEEDSFVFTCAPNDT
1h0h.1.A  --------------------------------------------------------------------AKQTTSVCCYCS

Target    HNCLLRAHV--KNGVIVRISPTYGYGKATDLAGNQASHRWDPRICQKGLILGRRIYGDRRVKAPMIRKGFKEWADAGFPR
1h0h.1.A  VGCGLIVHTDKKTNRAINVEGD------------PDHPINEGSLCAKGASTWQLAENERRPANPLYRA------------

Target    HDDGTPRADMEKRGYDEWLQIPWDEALAIAAKTLQNVAETYKGEDGAG-KLLEQGYEPAMVEAMHGAGVQAIKMRGGMPL
1h0h.1.A  ------------PGSDQWEEKSWDWMLDTIAERVAKTREATFVTKNAKGQVVNRC--------------DGIA-------

Target    LGAGRVFGFYRFANMLALLDGKLRPEAPPEEIVGSRAFDNYAWHTDLP--PGHPMVSGSQTVDFDLFAAEHSKLLVLIGM
1h0h.1.A  -----SVGSAAMDNEECWIYQAWLR------SLGLFYIEHQARIUHSATVAALAESYGRGAMTNHWIDLKNSDVILMMGS

Target    NWICTKMPDAHWIGDARLKGTRVVVISADYMPTANKADEIVILRPGTDTAFLLGVARELITKKLYDRDAVIQRTDLPLLV
1h0h.1.A  NPAENHPISFKWVMRAKDKGATLIHVDPRYTRTSTKCDLYAPLRSGSDIAFLNGMTKYILEKELYFKDYVVNYTNASFIV

Target    RLDTGERLSARDVFEGYRQAPLENYVALKTEEELAAPPSPPFTADKQVVPTELREEWGDFVYWDRATNGPAAVNRDEIGA
1h0h.1.A  GEGF---AFEEGLF----------------------------------------------AGYNKETRKYDKSKW-----

Target    KFAGDPALLGAFDVTLVDGTNVKARTAFSLLKEYLDENFDVQTTSEVCNVDPAAVRSLARQLAANK---GNALLAAGMGP
1h0h.1.A  --GFERDENGNP---KRDETLKHPRCVFQIMKKHYE-RYDLDKISAICGTPKELILKVYDAYCATGKPDKAGTIMYAMGW

Target    NHYFNADLFGRVHFLVAALTDNIGHFSGNVGSYAGNY--RGSLFQAMGQWIAENPFDQE---------A----DL----T
1h0h.1.A  TQHTVGVQNIRAMSINQLLLGNIGVAGGGVNALRGEANVQGST--DHGLLMHIYPGYLGTARASIPTYEEYTKKFTPVSK

Target    KPARVKRYFKS------ESAHYWNYGDR-------------PLVSPSEIITGKSHMPTPTKLIWFGNSNSLLGNAKWSFD
1h0h.1.A  DPQSANWWSNFPKYSASYIKSMWPDADLNEAYGYLPKGEDGKDYSWLTLFDDM--FQGKIKGFFAWGQNPACSGAN--SN

Target    VVKNTLPKQDAVFCNEWHWTSSCEYS-------------DLVFPADSWAEFKLPDMTASCTNPFLLAFPKTPLARIHNTR
1h0h.1.A  KTREALTKLDWMVNVNIFDNETGSFWRGPDMDPKKIKTEVFFLPCAVAIEKE--GSI-SNSGRWMQWRYV-GPEPRKNAI

Target    SDYEILAGVAAALADLVDEPRMKTYWKGILDGDPTPYLQRVLSGSNATRGILYEDLHASSAKGVPLLMNARTYPRHAGWE
1h0h.1.A  PDGDLIVELAKRVQK-----------------------------------------------------------------

Target    QRQEDKPWYTPTGRLEFYRPEPEWQAAGESLPIWREPVDATFYEPNAILANSKHPSINPRAPEDYGVPESQMDVETRQYR
1h0h.1.A  --------------------------------------------------------------------------------

Target    NVVRTWQELKLSKHPLTEKDPAYRFVFQTPKYRWGAHSTAVDSDWIAMLFGPFGDPYRRDSRTPWTGEAYAEINPRDAKE
1h0h.1.A  --------------------------------------------------------------------------------

Target    LGLKDGDYIWLDADPEDRPYRGADSSDEFYDVARAMMRVRIYSGMPRRVIRTWFNMYAATPGTVQAQKDVPGGPAQNQDT
1h0h.1.A  --------------------------------------------------------------------------------

Target    GYVALFRHGSHQSGTRAYLRPTQMTDSMNRKAYFGQTIGKGFEADVHSPSGAPKEGYVKVEKAEDGGDEGVGEWRPVTLG
1h0h.1.A  --------------------------------------------------------------------------------

Target    LRPDDPSEAMQAYLAGEFVTRKRKGS
1h0h.1.A  --------------------------

Model #04	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.14	0.44 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
3ir7.1.A	30.59	monomer	0.00	BLAST	X-ray	2.50Å	0.35	54 - 432	0.29	Respiratory nitrate reductase 1 alpha chain

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
6MO.4	Binding site not conserved.	MOLYBDENUM(VI) ION
AGA.5	Binding site not conserved.	(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
F3S.9	Binding site not conserved.	FE3-S4 CLUSTER
HEM.10	Binding site not conserved.	PROTOPORPHYRIN IX CONTAINING FE
HEM.11	Binding site not conserved.	PROTOPORPHYRIN IX CONTAINING FE
MD1.1	Binding site not conserved.	PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MD1.2	Binding site not conserved.	PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
SF4.3	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.6	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.7	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.8	Binding site not conserved.	IRON/SULFUR CLUSTER

Target    SDLSRRELLKRAVVVGTGAGLAELFLPAQFLSSASAQSEPQAVAIANPLAQMPDRSWERIYRDQFAEEDSFVFTCAPNDT
3ir7.1.A  -----------------------------------------------------NRDWEDGYRQRWQHDKIVRSTHGVNCT

Target    HNCLLRAHVKNGVIVRISPTYGYGKAT-DLAGNQASHRWDPRICQKGLILGRRIYGDRRVKAPMIRKGF-KEWADAGFPR
3ir7.1.A  GSCSWKIYVKNGLVTWETQQTDYPRTRPDLPNHE------PRGCPSGASYSWYLYSANRLKYPMMRKRLMKMWREAKALH

Target    HDDGTPRADMEKRGYDEWLQIPWDEALAIAAKTLQNVAETYKGEDGAGKLLEQGYEPAMVEAMHGAGVQAIKMRGGMPLL
3ir7.1.A  SDP-----------VEAWASIIED----------ADKAKSFKQARGRGGFVRSSWQ-EVNELIAASNVYTIKN------Y

Target    GAGRVFGFYRF--ANMLALLDGKLRPEAPPEEIVGSRAFDNYAWHTDLPPGHPMVSGSQTVDFDLFAAEHSKLLVLIGMN
3ir7.1.A  GPDRVAGFSPIPAMSMVSYASG-----ARYLSLIGGTCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGSN

Target    WICTKMPDAHWIGDARLKGTRVVVISADYMPTANKADEIVILRPGTDTAFLLGVARELITK------KLYDRDAVIQRTD
3ir7.1.A  VPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYTD

Target    LPLLVRLD-------TGERLSARDVFE--GYRQAPLENYVALKTEEELAAPPSPPFTADKQVVPTELREEWGDFVYWDRA
3ir7.1.A  MPMLVMLEERDGYYAAGRMLRAADLVDALGQENNPEWKTVAFNTNGEMVAP-----------------------------

Target    TNGPAAVNRDEIGAKFAGDPALLGAFDVTLVDGTNVKARTAFSLLKEYLDENFDVQTTSEVCNVDPAAVRSLARQLAANK
3ir7.1.A  --------------------------------------------------------------------------------

Target    GNALLAAGMGPNHYFNADLFGRVHFLVAALTDNIGHFSGNVGSYAGNYRGSLFQAMGQWIAENPFDQEADLTKPARVKRY
3ir7.1.A  --------------------------------------------------------------------------------

Target    FKSESAHYWNYGDRPLVSPSEIITGKSHMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPKQDAVFCNEWHWTSSCEYSD
3ir7.1.A  --------------------------------------------------------------------------------

Target    LVFPADSWAEFKLPDMTASCTNPFLLAFPKTPLARIHNTRSDYEILAGVAAALADLVDEPRMKTYWKGILDGDPTPYLQR
3ir7.1.A  --------------------------------------------------------------------------------

Target    VLSGSNATRGILYEDLHASSAKGVPLLMNARTYPRHAGWEQRQEDKPWYTPTGRLEFYRPEPEWQAAGESLPIWREPVDA
3ir7.1.A  --------------------------------------------------------------------------------

Target    TFYEPNAILANSKHPSINPRAPEDYGVPESQMDVETRQYRNVVRTWQELKLSKHPLTEKDPAYRFVFQTPKYRWGAHSTA
3ir7.1.A  --------------------------------------------------------------------------------

Target    VDSDWIAMLFGPFGDPYRRDSRTPWTGEAYAEINPRDAKELGLKDGDYIWLDADPEDRPYRGADSSDEFYDVARAMMRVR
3ir7.1.A  --------------------------------------------------------------------------------

Target    IYSGMPRRVIRTWFNMYAATPGTVQAQKDVPGGPAQNQDTGYVALFRHGSHQSGTRAYLRPTQMTDSMNRKAYFGQTIGK
3ir7.1.A  --------------------------------------------------------------------------------

Target    GFEADVHSPSGAPKEGYVKVEKAEDGGDEGVGEWRPVTLGLRPDDPSEAMQAYLAGEFVTRKRKGS
3ir7.1.A  ------------------------------------------------------------------

Model #05	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.11	0.38 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
6sdv.1.A	26.79	monomer	0.00	BLAST	X-ray	1.90Å	0.33	76 - 415	0.24	Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
GOL.6	Not biologically relevant.	GLYCEROL
GOL.7	Not biologically relevant.	GLYCEROL
GOL.8	Not biologically relevant.	GLYCEROL
GOL.9	Not biologically relevant.	GLYCEROL
GOL.10	Not biologically relevant.	GLYCEROL
GOL.11	Not biologically relevant.	GLYCEROL
GOL.12	Not biologically relevant.	GLYCEROL
GOL.13	Not biologically relevant.	GLYCEROL
GOL.14	Not biologically relevant.	GLYCEROL
GOL.15	Not biologically relevant.	GLYCEROL
H2S.5	Binding site not conserved.	HYDROSULFURIC ACID
MGD.1	Binding site not conserved.	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.2	Binding site not conserved.	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
NO3.16	Not biologically relevant.	NITRATE ION
NO3.17	Not biologically relevant.	NITRATE ION
PEG.18	Not biologically relevant.	DI(HYDROXYETHYL)ETHER
SF4.3	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.19	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.20	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.21	Binding site not conserved.	IRON/SULFUR CLUSTER
W.4	Not in contact with model.	TUNGSTEN ION

Target    SDLSRRELLKRAVVVGTGAGLAELFLPAQFLSSASAQSEPQAVAIANPLAQMPDRSWERIYRDQFAEEDSFVFTCAPNDT
6sdv.1.A  ---------------------------------------------------------------------------AKQTT

Target    HNCLLRAHVKNGVIVRISPTYGYGKATDLAGNQASHRWDPRICQKGLILGRRIYGDRRVKAPMIRKGFKEWADAGFPRHD
6sdv.1.A  SICCYCA-VGCGLIVHTAKD-GQGRAVNVEGDPDHPINEGSLCPKGASIFQLGENDQRGTQPLYRAPFS-----------

Target    DGTPRADMEKRGYDEWLQIPWDEALAIAAKTLQNVAE-TYKGEDGAGKLLEQGYEPAMVEAMHGAGVQAIKMRGGMPLLG
6sdv.1.A  -------------DTWKPVTWDFALTEIAKRIKKTRDASFTEKNAAGDLVNR------TEAIASFGSAAMDNEECWAYGN

Target    AGRVFGFYRFANMLALLDGKLRPEAPPEEIVGSRAFDNYAWHTDLPPGHPMVSGSQTVDFDLFAAEHSKLLVLIGMNWIC
6sdv.1.A  ILRSLG-------LVYIEHQARIUHSPTVPALAESFGR---------------GAMTNHWNDLA--NSDCILIMGSNAAE

Target    TKMPDAHWIGDARLKGTRVVVISADYMPTANKADEIVILRPGTDTAFLLGVARELITKKLYDRDAVIQRTDLPLLVRLDT
6sdv.1.A  NHPIAFKWVLRAKDKGATLIHVDPRFTRTSARCDVYAPIRSGADIPFLGGLIKYILDNKLYFTDYVREYTNASLIV----

Target    GERLSARD-VFEGYRQAPLENYVALKTEEELAAPPSPPFTADKQVVPTELREEWGDFVYWDRATNGPAAVNRDEIGAKFA
6sdv.1.A  GEKFSFKDGLFSGYDAA---------------------------------------------------------------

Target    GDPALLGAFDVTLVDGTNVKARTAFSLLKEYLDENFDVQTTSEVCNVDPAAVRSLARQLAANKGNALLAAGMGPNHYFNA
6sdv.1.A  --------------------------------------------------------------------------------

Target    DLFGRVHFLVAALTDNIGHFSGNVGSYAGNYRGSLFQAMGQWIAENPFDQEADLTKPARVKRYFKSESAHYWNYGDRPLV
6sdv.1.A  --------------------------------------------------------------------------------

Target    SPSEIITGKSHMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPKQDAVFCNEWHWTSSCEYSDLVFPADSWAEFKLPDMT
6sdv.1.A  --------------------------------------------------------------------------------

Target    ASCTNPFLLAFPKTPLARIHNTRSDYEILAGVAAALADLVDEPRMKTYWKGILDGDPTPYLQRVLSGSNATRGILYEDLH
6sdv.1.A  --------------------------------------------------------------------------------

Target    ASSAKGVPLLMNARTYPRHAGWEQRQEDKPWYTPTGRLEFYRPEPEWQAAGESLPIWREPVDATFYEPNAILANSKHPSI
6sdv.1.A  --------------------------------------------------------------------------------

Target    NPRAPEDYGVPESQMDVETRQYRNVVRTWQELKLSKHPLTEKDPAYRFVFQTPKYRWGAHSTAVDSDWIAMLFGPFGDPY
6sdv.1.A  --------------------------------------------------------------------------------

Target    RRDSRTPWTGEAYAEINPRDAKELGLKDGDYIWLDADPEDRPYRGADSSDEFYDVARAMMRVRIYSGMPRRVIRTWFNMY
6sdv.1.A  --------------------------------------------------------------------------------

Target    AATPGTVQAQKDVPGGPAQNQDTGYVALFRHGSHQSGTRAYLRPTQMTDSMNRKAYFGQTIGKGFEADVHSPSGAPKEGY
6sdv.1.A  --------------------------------------------------------------------------------

Target    VKVEKAEDGGDEGVGEWRPVTLGLRPDDPSEAMQAYLAGEFVTRKRKGS
6sdv.1.A  -------------------------------------------------

Model #06	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.08	0.40 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
7l5i.1.A	24.11	monomer	0.00	BLAST	X-ray	1.73Å	0.34	128 - 389	0.19	Trimethylamine-N-oxide reductase

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
CL.6	Not biologically relevant.	CHLORIDE ION
EPE.1	Not biologically relevant.	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
EPE.2	Not biologically relevant.	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
EPE.7	Not biologically relevant.	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
MGD.3	Binding site not conserved.	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.4	Binding site not conserved.	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MO.5	Binding site not conserved.	MOLYBDENUM ATOM
O.8	Binding site not conserved.	OXYGEN ATOM

Target    SDLSRRELLKRAVVVGTGAGLAELFLPAQFLSSASAQSEPQAVAIANPLAQMPDRSWERIYRDQFAEEDSFVFTCAPNDT
7l5i.1.A  --------------------------------------------------------------------------------

Target    HNCLLRAHVKNGVIVRISPTYGYGKATDLAGNQASHRWDPRICQKGLILGRRIYGDRRVKAPMIRKGFKEWADAGFPRHD
7l5i.1.A  -----------------------------------------------VVADQLYSEARVKCPMVRKGF--LANPG-----

Target    DGTPRADMEKRGYDEWLQIPWDEALAIAAKTLQNVAETYKGEDGAGKLLEQGYEPAMVEAMHGAGVQAIKMRGGMPLLGA
7l5i.1.A  ----KSDTTMRGRDEWVRVSWDEALDLVHNQLKRV----RDEHGSTGIFAGSYGWFSCGSLH-----------------A

Target    GRVFGFYRFANMLALLDG-KLRPEAPPEEIVGSRAFDNYAWHTDLPPGHPMVSGSQTVDFDLFAAEHSKLLVLIGMNWIC
7l5i.1.A  SRTL-LQRYMNATGGFVGHKGDYSTGAAQVIMPHVLGTIEVYEQQTSWESILESS-----DIIVLWSANPLTTMRIAWMS

Target    TKMPDAHWIGDARLKGTRVVVISADYMPTANKAD-EIVILRPGTDTAFLLGVARELITKKLYDRDAVIQRTDLPLLVRLD
7l5i.1.A  TDQKGIEYFKKFQASGKRIICIDPQKSETCQMLNAEWIPVNTATDVPLMLGIAHTLVEQGKHDKDFLKKYT---------

Target    TGERLSARDVFEGYRQAPLENYVALKTEEELAAPPSPPFTADKQVVPTELREEWGDFVYWDRATNGPAAVNRDEIGAKFA
7l5i.1.A  --------------------------------------------------------------------------------

Target    GDPALLGAFDVTLVDGTNVKARTAFSLLKEYLDENFDVQTTSEVCNVDPAAVRSLARQLAANKGNALLAAGMGPNHYFNA
7l5i.1.A  --------------------------------------------------------------------------------

Target    DLFGRVHFLVAALTDNIGHFSGNVGSYAGNYRGSLFQAMGQWIAENPFDQEADLTKPARVKRYFKSESAHYWNYGDRPLV
7l5i.1.A  --------------------------------------------------------------------------------

Target    SPSEIITGKSHMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPKQDAVFCNEWHWTSSCEYSDLVFPADSWAEFKLPDMT
7l5i.1.A  --------------------------------------------------------------------------------

Target    ASCTNPFLLAFPKTPLARIHNTRSDYEILAGVAAALADLVDEPRMKTYWKGILDGDPTPYLQRVLSGSNATRGILYEDLH
7l5i.1.A  --------------------------------------------------------------------------------

Target    ASSAKGVPLLMNARTYPRHAGWEQRQEDKPWYTPTGRLEFYRPEPEWQAAGESLPIWREPVDATFYEPNAILANSKHPSI
7l5i.1.A  --------------------------------------------------------------------------------

Target    NPRAPEDYGVPESQMDVETRQYRNVVRTWQELKLSKHPLTEKDPAYRFVFQTPKYRWGAHSTAVDSDWIAMLFGPFGDPY
7l5i.1.A  --------------------------------------------------------------------------------

Target    RRDSRTPWTGEAYAEINPRDAKELGLKDGDYIWLDADPEDRPYRGADSSDEFYDVARAMMRVRIYSGMPRRVIRTWFNMY
7l5i.1.A  --------------------------------------------------------------------------------

Target    AATPGTVQAQKDVPGGPAQNQDTGYVALFRHGSHQSGTRAYLRPTQMTDSMNRKAYFGQTIGKGFEADVHSPSGAPKEGY
7l5i.1.A  --------------------------------------------------------------------------------

Target    VKVEKAEDGGDEGVGEWRPVTLGLRPDDPSEAMQAYLAGEFVTRKRKGS
7l5i.1.A  -------------------------------------------------

Model #07	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.07	0.36 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
1eu1.1.A	33.04	monomer	0.00	BLAST	X-ray	1.30Å	0.36	133 - 401	0.19	DIMETHYL SULFOXIDE REDUCTASE

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
6MO.8	Binding site not conserved.	MOLYBDENUM(VI) ION
CD.5	Binding site not conserved.	CADMIUM ION
EPE.11	Not biologically relevant.	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
GLC.1	Not in contact with model.	alpha-D-glucopyranose
GLC.2	Binding site not conserved.	alpha-D-glucopyranose
GLC.3	Binding site not conserved.	alpha-D-glucopyranose
MGD.6	Binding site not conserved.	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.7	Binding site not conserved.	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
O.9	Binding site not conserved.	OXYGEN ATOM
O.10	Binding site not conserved.	OXYGEN ATOM
SO4.4	Not biologically relevant.	SULFATE ION

Target    SDLSRRELLKRAVVVGTGAGLAELFLPAQFLSSASAQSEPQAVAIANPLAQMPDRSWERIYRDQFAEEDSFVFTCAPNDT
1eu1.1.A  --------------------------------------------------------------------------------

Target    HNCLLRAHVKNGVIVRISPTYGYGKATDLAGNQASHRWDPRICQKGLILGRRIYGDRRVKAPMIRKGFKEWADAGFPRHD
1eu1.1.A  ----------------------------------------------------IYSPTRIKYPMVRREFLEKG--------

Target    DGTPRADMEKRGYDEWLQIPWDEALAIAAKTLQNVAETYKGEDGAGKLLEQGYEPAMVEAMHGAGVQAIKMRGGMPLLGA
1eu1.1.A  ---VNADRSTRGNGDFVRVTWDEALDLVARELKRVQESY----GPTGTFGGSYGWKSPGRLHNCQVL---MRRALNLAG-

Target    GRVFGFYRFANMLALLDGKLRPEAPPEEIVGSRAFDNYAWHTDLPPGHPMVSGSQTVDFDLFAAEHSKLLVL-----IGM
1eu1.1.A  GFVNSSGDYSTAAAQI---IMP-----HVMGT--LEVYEQQTAWP----------------VVVENTDLMVFWAADPMKT

Target    NWICTKMPD-AHWIGDARLK--GTRVVVISADYMPTANK-ADEIVILRPGTDTAFLLGVARELITKKLYDRDAVIQ-RTD
1eu1.1.A  NEIGWVIPDHGAYAGMKALKEKGTRVICINPVRTETADYFGADVVSPRPQTDVALMLGMAHTLYSEDLHDKDFLENCTTG

Target    LPLLVRLDTGERLSARDVFEGYRQAPLENYVALKTEEELAAPPSPPFTADKQVVPTELREEWGDFVYWDRATNGPAAVNR
1eu1.1.A  FDLFAAYLTGE---------------------------------------------------------------------

Target    DEIGAKFAGDPALLGAFDVTLVDGTNVKARTAFSLLKEYLDENFDVQTTSEVCNVDPAAVRSLARQLAANKGNALLAAGM
1eu1.1.A  --------------------------------------------------------------------------------

Target    GPNHYFNADLFGRVHFLVAALTDNIGHFSGNVGSYAGNYRGSLFQAMGQWIAENPFDQEADLTKPARVKRYFKSESAHYW
1eu1.1.A  --------------------------------------------------------------------------------

Target    NYGDRPLVSPSEIITGKSHMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPKQDAVFCNEWHWTSSCEYSDLVFPADSWA
1eu1.1.A  --------------------------------------------------------------------------------

Target    EFKLPDMTASCTNPFLLAFPKTPLARIHNTRSDYEILAGVAAALADLVDEPRMKTYWKGILDGDPTPYLQRVLSGSNATR
1eu1.1.A  --------------------------------------------------------------------------------

Target    GILYEDLHASSAKGVPLLMNARTYPRHAGWEQRQEDKPWYTPTGRLEFYRPEPEWQAAGESLPIWREPVDATFYEPNAIL
1eu1.1.A  --------------------------------------------------------------------------------

Target    ANSKHPSINPRAPEDYGVPESQMDVETRQYRNVVRTWQELKLSKHPLTEKDPAYRFVFQTPKYRWGAHSTAVDSDWIAML
1eu1.1.A  --------------------------------------------------------------------------------

Target    FGPFGDPYRRDSRTPWTGEAYAEINPRDAKELGLKDGDYIWLDADPEDRPYRGADSSDEFYDVARAMMRVRIYSGMPRRV
1eu1.1.A  --------------------------------------------------------------------------------

Target    IRTWFNMYAATPGTVQAQKDVPGGPAQNQDTGYVALFRHGSHQSGTRAYLRPTQMTDSMNRKAYFGQTIGKGFEADVHSP
1eu1.1.A  --------------------------------------------------------------------------------

Target    SGAPKEGYVKVEKAEDGGDEGVGEWRPVTLGLRPDDPSEAMQAYLAGEFVTRKRKGS
1eu1.1.A  ---------------------------------------------------------

Materials and Methods

Template Search

Template search with has been performed against the SWISS-MODEL template library (SMTL, last update: 2023-03-23, last included PDB release: 2023-03-17).

Template Selection

For each identified template, the template's quality has been predicted from features of the target-template alignment. The templates with the highest quality have then been selected for model building.

Model Building

Models are built based on the target-template alignment using ProMod3 (Studer et al.). Coordinates which are conserved between the target and the template are copied from the template to the model. Insertions and deletions are remodelled using a fragment library. Side chains are then rebuilt. Finally, the geometry of the resulting model is regularized by using a force field.

Model Quality Estimation

The global and per-residue model quality has been assessed using the QMEAN scoring function (Studer et al.).

Ligand Modelling

Ligands present in the template structure are transferred by homology to the model when the following criteria are met: (a) The ligands are annotated as biologically relevant in the template library, (b) the ligand is in contact with the model, (c) the ligand is not clashing with the protein, (d) the residues in contact with the ligand are conserved between the target and the template. If any of these four criteria is not satisfied, a certain ligand will not be included in the model. The model summary includes information on why and which ligand has not been included.

Oligomeric State Conservation

The quaternary structure annotation of the template is used to model the target sequence in its oligomeric form. The method (Bertoni et al.) is based on a supervised machine learning algorithm, Support Vector Machines (SVM), which combines interface conservation, structural clustering, and other template features to provide a quaternary structure quality estimate (QSQE). The QSQE score is a number between 0 and 1, reflecting the expected accuracy of the interchain contacts for a model built based a given alignment and template. Higher numbers indicate higher reliability. This complements the GMQE score which estimates the accuracy of the tertiary structure of the resulting model.

References

BLAST
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L. BLAST+: architecture and applications. BMC Bioinformatics 10, 421-430 (2009).
HHblits
Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J., Söding, J. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20, 473 (2019).

Table T1:

Primary amino acid sequence for which templates were searched and models were built.

SDLSRRELLKRAVVVGTGAGLAELFLPAQFLSSASAQSEPQAVAIANPLAQMPDRSWERIYRDQFAEEDSFVFTCAPNDTHNCLLRAHVKNGVIVRISPT
YGYGKATDLAGNQASHRWDPRICQKGLILGRRIYGDRRVKAPMIRKGFKEWADAGFPRHDDGTPRADMEKRGYDEWLQIPWDEALAIAAKTLQNVAETYK
GEDGAGKLLEQGYEPAMVEAMHGAGVQAIKMRGGMPLLGAGRVFGFYRFANMLALLDGKLRPEAPPEEIVGSRAFDNYAWHTDLPPGHPMVSGSQTVDFD
LFAAEHSKLLVLIGMNWICTKMPDAHWIGDARLKGTRVVVISADYMPTANKADEIVILRPGTDTAFLLGVARELITKKLYDRDAVIQRTDLPLLVRLDTG
ERLSARDVFEGYRQAPLENYVALKTEEELAAPPSPPFTADKQVVPTELREEWGDFVYWDRATNGPAAVNRDEIGAKFAGDPALLGAFDVTLVDGTNVKAR
TAFSLLKEYLDENFDVQTTSEVCNVDPAAVRSLARQLAANKGNALLAAGMGPNHYFNADLFGRVHFLVAALTDNIGHFSGNVGSYAGNYRGSLFQAMGQW
IAENPFDQEADLTKPARVKRYFKSESAHYWNYGDRPLVSPSEIITGKSHMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPKQDAVFCNEWHWTSSCEYS
DLVFPADSWAEFKLPDMTASCTNPFLLAFPKTPLARIHNTRSDYEILAGVAAALADLVDEPRMKTYWKGILDGDPTPYLQRVLSGSNATRGILYEDLHAS
SAKGVPLLMNARTYPRHAGWEQRQEDKPWYTPTGRLEFYRPEPEWQAAGESLPIWREPVDATFYEPNAILANSKHPSINPRAPEDYGVPESQMDVETRQY
RNVVRTWQELKLSKHPLTEKDPAYRFVFQTPKYRWGAHSTAVDSDWIAMLFGPFGDPYRRDSRTPWTGEAYAEINPRDAKELGLKDGDYIWLDADPEDRP
YRGADSSDEFYDVARAMMRVRIYSGMPRRVIRTWFNMYAATPGTVQAQKDVPGGPAQNQDTGYVALFRHGSHQSGTRAYLRPTQMTDSMNRKAYFGQTIG
KGFEADVHSPSGAPKEGYVKVEKAEDGGDEGVGEWRPVTLGLRPDDPSEAMQAYLAGEFVTRKRKGS

Table T2:

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Coverage	Description
7b04.1.B	40.77	monomer	-	BLAST	X-ray	2.97Å	0.41	0.96	Nitrite oxidoreductase subunit A
7b04.1.B	39.64	monomer	-	HHblits	X-ray	2.97Å	0.40	0.96	Nitrite oxidoreductase subunit A
7b04.2.B	40.77	monomer	-	BLAST	X-ray	2.97Å	0.41	0.96	Nitrite oxidoreductase subunit A
7b04.2.B	39.64	monomer	-	HHblits	X-ray	2.97Å	0.40	0.96	Nitrite oxidoreductase subunit A
4ydd.1.A	25.48	monomer	-	HHblits	X-ray	1.86Å	0.33	0.71	DMSO reductase family type II enzyme, molybdopterin subunit
5e7o.1.A	25.82	monomer	-	HHblits	X-ray	2.40Å	0.33	0.71	DMSO reductase family type II enzyme, molybdopterin subunit
3ir5.1.A	24.12	monomer	-	HHblits	X-ray	2.30Å	0.32	0.78	Respiratory nitrate reductase 1 alpha chain
1r27.4.A	23.96	homo-dimer	0.14	HHblits	X-ray	2.00Å	0.32	0.80	Respiratory nitrate reductase 1 alpha chain
2ivf.1.A	24.43	monomer	-	HHblits	X-ray	1.88Å	0.32	0.75	ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
3egw.1.A	24.12	homo-dimer	0.12	HHblits	X-ray	1.90Å	0.32	0.78	Respiratory nitrate reductase 1 alpha chain
3ir7.1.A	23.85	monomer	-	HHblits	X-ray	2.50Å	0.32	0.80	Respiratory nitrate reductase 1 alpha chain
1q16.1.A	24.04	monomer	-	HHblits	X-ray	1.90Å	0.32	0.78	Respiratory nitrate reductase 1 alpha chain
3ir6.1.A	23.85	monomer	-	HHblits	X-ray	2.80Å	0.32	0.80	Respiratory nitrate reductase 1 alpha chain
5e7o.1.A	28.33	monomer	-	BLAST	X-ray	2.40Å	0.34	0.60	DMSO reductase family type II enzyme, molybdopterin subunit
4ydd.1.A	28.33	monomer	-	BLAST	X-ray	1.86Å	0.35	0.60	DMSO reductase family type II enzyme, molybdopterin subunit
1e60.1.A	20.00	monomer	-	HHblits	X-ray	2.00Å	0.30	0.63	Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e18.1.A	19.86	monomer	-	HHblits	X-ray	2.00Å	0.30	0.63	DMSO REDUCTASE.
1e5v.2.A	19.84	monomer	-	HHblits	X-ray	2.40Å	0.30	0.63	Dimethyl sulfoxide/trimethylamine N-oxide reductase
4dmr.1.A	20.06	monomer	-	HHblits	X-ray	1.90Å	0.30	0.59	DMSO REDUCTASE
1dms.1.A	20.64	monomer	-	HHblits	X-ray	1.88Å	0.30	0.59	DMSO REDUCTASE
1h0h.1.A	17.09	monomer	-	HHblits	X-ray	1.80Å	0.28	0.47	FORMATE DEHYDROGENASE SUBUNIT ALPHA
2ivf.1.A	36.10	monomer	-	BLAST	X-ray	1.88Å	0.38	0.38	ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
6q8o.1.C	17.17	monomer	-	HHblits	X-ray	3.61Å	0.27	0.42	NADH-quinone oxidoreductase subunit 3
3m9s.1.C	17.17	monomer	-	HHblits	X-ray	4.50Å	0.27	0.42	NADH-quinone oxidoreductase subunit 3
6ziy.1.C	17.17	monomer	-	HHblits	EM	NA	0.27	0.42	NADH-quinone oxidoreductase subunit 3
6zjl.1.C	17.17	monomer	-	HHblits	EM	NA	0.27	0.42	NADH-quinone oxidoreductase subunit 3
6zjn.1.C	17.17	monomer	-	HHblits	EM	NA	0.27	0.42	NADH-quinone oxidoreductase subunit 3
2fug.2.C	17.17	monomer	-	HHblits	X-ray	3.30Å	0.27	0.42	NADH-quinone oxidoreductase chain 3
6zjy.1.C	17.17	monomer	-	HHblits	EM	NA	0.27	0.42	NADH-quinone oxidoreductase subunit 3
6zk9.1.C	14.65	monomer	-	HHblits	EM	NA	0.27	0.33	NADH:ubiquinone oxidoreductase core subunit S1
7zd6.1.4	14.40	monomer	-	HHblits	EM	NA	0.27	0.33	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6qcf.1.C	14.40	monomer	-	HHblits	EM	NA	0.27	0.33	NADH:ubiquinone oxidoreductase core subunit S1
6qc5.1.C	14.40	monomer	-	HHblits	EM	NA	0.27	0.33	NADH:ubiquinone oxidoreductase core subunit S1
7qsd.1.G	14.65	monomer	-	HHblits	EM	NA	0.27	0.33	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
5o31.1.8	14.91	monomer	-	HHblits	EM	4.13Å	0.27	0.33	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7dgr.10.A	14.91	monomer	-	HHblits	EM	NA	0.27	0.33	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
3ir7.1.A	30.59	monomer	-	BLAST	X-ray	2.50Å	0.35	0.29	Respiratory nitrate reductase 1 alpha chain
3ir5.1.A	30.88	monomer	-	BLAST	X-ray	2.30Å	0.36	0.29	Respiratory nitrate reductase 1 alpha chain
1r27.4.A	30.59	homo-dimer	-	BLAST	X-ray	2.00Å	0.36	0.29	Respiratory nitrate reductase 1 alpha chain
1q16.1.A	30.59	monomer	-	BLAST	X-ray	1.90Å	0.36	0.29	Respiratory nitrate reductase 1 alpha chain
3egw.1.A	30.59	homo-dimer	-	BLAST	X-ray	1.90Å	0.35	0.29	Respiratory nitrate reductase 1 alpha chain
3ir6.1.A	30.59	monomer	-	BLAST	X-ray	2.80Å	0.36	0.29	Respiratory nitrate reductase 1 alpha chain
6sdv.1.A	26.79	monomer	-	BLAST	X-ray	1.90Å	0.33	0.24	Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit
6sdr.1.A	26.79	monomer	-	BLAST	X-ray	2.10Å	0.33	0.24	Formate dehydrogenase, alpha subunit, selenocysteine-containing
8bqg.1.A	26.79	monomer	-	BLAST	X-ray	1.95Å	0.33	0.24	Formate dehydrogenase, alpha subunit, selenocysteine-containing
7l5i.1.A	24.11	monomer	-	BLAST	X-ray	1.73Å	0.34	0.19	Trimethylamine-N-oxide reductase
7l5s.1.A	24.11	monomer	-	BLAST	X-ray	2.09Å	0.34	0.19	Trimethylamine-N-oxide reductase
4dmr.1.A	29.09	monomer	-	BLAST	X-ray	1.90Å	0.35	0.19	DMSO REDUCTASE
1e18.1.A	29.09	monomer	-	BLAST	X-ray	2.00Å	0.35	0.19	DMSO REDUCTASE.
1eu1.1.A	33.04	monomer	-	BLAST	X-ray	1.30Å	0.36	0.19	DIMETHYL SULFOXIDE REDUCTASE

The table above shows the top 50 filtered templates. A further 372 templates were found which were considered to be less suitable for modelling than the filtered list.
1aa6.1.A, 1be3.1.E, 1bgy.1.P, 1cz4.1.A, 1cz5.1.A, 1dms.1.A, 1e18.1.A, 1e5v.2.A, 1e60.1.A, 1eu1.1.A, 1fdo.1.A, 1g8j.1.A, 1g8k.1.A, 1h0h.1.A, 1ici.1.A, 1jeo.1.A, 1kb9.1.E, 1kqf.1.A, 1l0l.1.E, 1l0n.1.E, 1m2g.1.A, 1m2h.1.A, 1m2j.1.A, 1m2k.1.A, 1m2n.1.A, 1m2n.1.B, 1ma3.1.A, 1ntk.1.E, 1ntm.1.E, 1ogy.1.A, 1q16.1.A, 1q90.1.E, 1r27.4.A, 1s5p.1.A, 1s7g.1.A, 1s7g.1.B, 1s7g.1.C, 1s7g.1.D, 1s7g.1.E, 1sqb.1.E, 1sqp.1.P, 1sqq.1.P, 1sqv.1.E, 1tmo.1.A, 1uhd.1.B, 1uhe.1.B, 1vf5.1.D, 1vf5.1.L, 1wlf.1.A, 1x94.1.A, 1x94.1.B, 1yc5.1.A, 1zrt.1.C, 1zrt.1.F, 2a3n.1.A, 2b4y.1.A, 2b4y.3.A, 2d2c.1.D, 2d2c.1.L, 2e75.1.D, 2e76.1.D, 2e7z.1.A, 2fyn.1.C, 2fyn.2.C, 2fyu.1.E, 2h2i.1.A, 2h4h.1.A, 2h59.1.B, 2i2w.1.A, 2i2w.2.B, 2iv2.1.A, 2ivf.1.A, 2ki8.1.A, 2nya.1.A, 2nyr.1.A, 2nyr.1.B, 2pjh.1.B, 2pq4.1.B, 2qjk.1.C, 2qjp.1.C, 2qjy.3.F, 2v3v.1.A, 2v45.1.A, 2vpx.1.D, 2vpz.1.A, 2x3y.1.A, 2ybb.1.b, 3cwb.1.E, 3egw.1.A, 3etn.1.A, 3eua.1.A, 3fj1.1.A, 3h1h.1.E, 3h1h.1.O, 3h1i.1.E, 3ir5.1.A, 3ir6.1.A, 3ir7.1.A, 3jr3.1.A, 3k35.1.A, 3l75.1.E, 3l75.1.O, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3pki.1.A, 3plx.1.B, 3qc8.1.A, 3qq7.1.A, 3qq8.1.A, 3qwz.1.A, 3riy.2.A, 3sho.1.A, 3sho.1.C, 3tiw.1.A, 3tiw.2.A, 3zg6.1.A, 4aay.1.A, 4aok.1.B, 4aok.1.D, 4bv2.3.A, 4dmr.1.A, 4g1c.1.A, 4g1c.2.A, 4ga5.1.A, 4ga6.1.A, 4h44.1.D, 4hda.1.A, 4hda.2.A, 4ivn.1.A, 4kdi.1.A, 4kdi.2.A, 4kdl.1.A, 4ogq.1.L, 4pv1.1.L, 4rv0.1.A, 4twi.1.A, 4twj.1.A, 4u3f.1.E, 4utn.1.A, 4utn.2.A, 4v4c.1.A, 4wd3.1.A, 4ydd.1.A, 5b6c.1.A, 5bwl.1.A, 5cuo.1.A, 5cup.1.A, 5e7o.1.A, 5e7p.1.A, 5epp.1.A, 5g4f.1.A, 5g4f.1.B, 5g4f.1.C, 5g4f.1.D, 5g4f.1.E, 5g4f.1.F, 5glf.1.A, 5glf.2.A, 5glf.3.A, 5glf.4.A, 5gpn.24.A, 5j8k.55.A, 5kkz.1.C, 5kli.1.C, 5klv.1.P, 5ls7.1.L, 5ltz.1.A, 5lu5.1.A, 5lu6.1.A, 5lu7.1.A, 5mf6.1.A, 5nqd.1.A, 5o31.1.8, 5oj7.1.A, 5ojn.1.A, 5okd.1.E, 5t5i.1.B, 5t5i.1.D, 5x16.1.A, 5x4l.1.A, 5x4l.2.A, 5xhs.1.A, 5xtb.1.L, 5xte.1.C, 5y2f.1.A, 6aco.1.A, 6acp.1.A, 6adq.1.L, 6btm.1.B, 6cz7.1.A, 6enx.1.A, 6eo0.1.A, 6eqs.3.A, 6f0k.1.B, 6fky.1.A, 6fky.2.A, 6flg.1.A, 6g72.1.G, 6gcs.1.A, 6giq.1.E, 6hd3.1.A, 6hu9.1.E, 6hwh.1.A, 6ljk.1.A, 6ljm.1.A, 6lod.1.B, 6nhg.1.E, 6nin.1.C, 6q9e.1.E, 6q9e.1.O, 6qbx.15.A, 6qbx.5.A, 6qc2.33.A, 6qc2.43.A, 6qc3.15.A, 6qc3.5.A, 6qc4.15.A, 6qc4.5.A, 6qc5.1.C, 6qcf.1.C, 6rfq.1.A, 6rfs.1.A, 6rqf.1.D, 6rqf.1.L, 6rxj.1.A, 6rxm.1.A, 6rxm.2.A, 6rxm.3.A, 6rxm.4.A, 6rxm.5.A, 6rxm.6.A, 6rxo.1.A, 6rxo.2.A, 6rxp.2.A, 6rxq.4.A, 6rxs.1.A, 6s6y.1.B, 6sdr.1.A, 6sdv.1.A, 6t0b.1.E, 6t0b.1.O, 6t15.1.E, 6t15.1.O, 6tg9.1.A, 6x89.1.H, 6xvg.3.A, 6yj4.1.G, 6ymx.1.Q, 6ymx.1.Z, 6zk9.1.C, 6zr2.1.G, 7a23.1.O, 7ak5.1.G, 7ak6.1.G, 7aqr.1.F, 7ar7.1.G, 7ar8.1.G, 7arc.1.F, 7b04.1.B, 7b04.2.B, 7bkb.1.F, 7bkb.1.J, 7bkb.1.L, 7cl0.1.A, 7dbo.1.A, 7dbo.2.A, 7dg7.1.A, 7dg9.1.A, 7dgr.10.A, 7dgr.60.A, 7dgs.50.A, 7dgs.60.A, 7di0.1.A, 7di0.2.A, 7di0.3.A, 7di1.1.A, 7du6.1.A, 7du7.1.A, 7dvc.1.A, 7dvc.5.A, 7dvf.1.A, 7dvh.1.A, 7dvh.2.A, 7dvh.4.A, 7dww.1.A, 7dww.2.A, 7dxr.1.A, 7dxr.1.B, 7dxr.2.B, 7dxs.1.A, 7dxs.1.B, 7dxs.2.A, 7dxs.2.B, 7dxt.1.A, 7dxu.1.A, 7dxu.1.B, 7dxu.2.B, 7dxv.1.A, 7dxv.1.B, 7dxw.1.A, 7dxx.1.A, 7dxx.1.B, 7dxy.1.A, 7dxz.1.A, 7dxz.2.A, 7dxz.2.B, 7dxz.3.A, 7dyc.1.A, 7dyc.2.A, 7dyc.3.A, 7e1v.1.P, 7e5z.1.A, 7en5.1.A, 7en6.1.A, 7en6.1.B, 7en6.1.C, 7en6.1.D, 7jrg.1.E, 7l5i.1.A, 7l5s.1.A, 7nz1.1.E, 7o37.1.E, 7o37.1.O, 7o3c.1.E, 7o3c.1.O, 7o3h.1.E, 7o3h.1.O, 7p61.1.C, 7p63.1.C, 7q5y.1.A, 7qrm.1.D, 7qsd.1.G, 7qv7.1.L, 7qv7.1.O, 7r0w.1.L, 7r0w.1.Q, 7rh5.1.V, 7rja.1.H, 7rjb.1.I, 7t2r.1.A, 7t30.1.A, 7tce.2.F, 7tgh.58.A, 7tlj.1.C, 7tz6.1.E, 7tz6.1.P, 7v2c.1.L, 7vw6.1.A, 7vxu.1.L, 7wbb.1.A, 7wbb.1.B, 7wbb.1.C, 7wbb.1.D, 7wbb.1.E, 7wbb.1.G, 7z0t.1.G, 7zd6.1.4, 7zm7.1.I, 7zxy.1.D, 7zxy.1.L, 8asi.1.A, 8asi.1.E, 8asj.1.E, 8b9z.1.G, 8ba0.1.G, 8bel.1.B, 8bel.1.I, 8bpx.51.A, 8bqg.1.A, 8e73.55.A, 8e9g.1.G

Model Building Report

Results

Models

Model #01

Included Ligands

Excluded ligands

Model #02

Excluded ligands

Model #03

Excluded ligands

Model #04

Excluded ligands

Model #05

Excluded ligands

Model #06

Excluded ligands

Model #07

Excluded ligands

Materials and Methods

Template Search

Template Selection

Model Building

Model Quality Estimation

Ligand Modelling

Oligomeric State Conservation

References

Table T1:

Table T2: