Untitled Project

SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "Untitled Project" submitted to SWISS-MODEL workspace on March 29, 2023, 4:10 a.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 515 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;	0.79	0.80 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
7b04.1.B	57.58	monomer	0.00	HHblits	X-ray	2.97Å	0.48	28 - 1144	1.00	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    MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAF
7b04.1.B  MKLTRRAFLQVAGATGATLTLAKNAMAFRLLKPAVVVDNPLDTYPDRRWESVYRDQYQYDRTFTYCCSPNDTHACRIRAF

Target    VRNGVVMRVEQNYDHQTYEDLYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGWKQWMDDNAPELTAETKRKYK
7b04.1.B  VRNNVMMRVEQNYDHQNYSDLYGNKATRNWNPRMCLKGYTFHRRVYGPYRLRYPLIRKGWKRWADDGFPELTPENKTKYM

Target    FDSRFLDDMLRVSWDTAFTYAAKAMITIATRY-SGEAGARRLREQGYAPEMIEMMKGAGTRCFKHRAGMPVLGIIGKMGN
7b04.1.B  FDNRGNDELLRASWDEAFTYASKGIIHITKKYSGPEGAQK-LIDQGYPKEMVDRMQGAGTRTFKGRGGMGLLGVIGKYGM

Target    TRMNGGINALLDTWIRKVSPDQAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFSKLNTSWGKNFVENKMPEAH
7b04.1.B  YRFNNC-LAIVDAHNRGVGPDQALGGRNWSNYTWHGDQAPGHPFSHGLQTSDVDMNDVRFSKLLIQTGKNLIENKMPEAH

Target    WKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENMHDIDFLKSFTDAPILVRTDTLQYLDPR
7b04.1.B  WVTEVMERGGKIVVITPEYSPSAQKADYWIPIRNNTDTALFLGITKILIDNKWYDADYVKKFTDFPLLIRTDTLKRVSPK

Target    DVIADYKFPDFSKSYSGRIQSLKPEQIQRLGGMMVWDLNKKQVVPLHREQVGWHYTNSGIDAALTGTYRVKLLNGREIDA
7b04.1.B  DIIPNYKLQDISDGPSYHIQGLKDEQREIIGDFVVWDAKSKGPKAITRDDVGETLVKKGIDPVLEGSFKLKTIDGKEIEV

Target    MPIWQMYMVHFQDYDLDTVHQITRTPKDLIVRWARDSGTIKPAAIHNGEGTCHYFHQTANARGAAMVLIITGNVGKFGTG
7b04.1.B  MTLLEMYKIHLRDYDIDSVVSMTNSPKDLIERLAKDIATIKPVAIHYGEGVNHYFHATLMNRSYYLPVMLTGNVGYFGSG

Target    QHTWAGNYKAGTWTATPWSGAGLSVHTGEDPFNITLDPNAHGKEIKTRSYYYGEEVGYWNHGDTALIVNTPKYGRKVFTG
7b04.1.B  SHTWAGNYKAGNFQASKWSGPGFYGWVAEDVFKPNLDPYASAKDLNIKGRALDEEVAYWNHSERPLIVNTPKYGRKVFTG

Target    KTHMPTPSKFRWVVNVNVVNNAKHHYDMVRNVDPNIECLITQDIEMTSDINHADIAFAANSWMEFTYPEMTVTVSNPWVQ
7b04.1.B  KTHMPSPTKVLWFTNVNLINNAKHVYQMLKNVNPNIEQIMSTDIEITGSIEYADFAFPANSWVEFQEFEITNSCSNPFIQ

Target    IWK-GGIRPLYDTRNDLDTFAGVAAKLSDMTGDKRMRDYFAMVYQNRVDVYVQRMLDASSTFYGYSADVMLKSE---KGW
7b04.1.B  IWGKTGITPVYESKDDVKILAGMASKLGELLRDKRFEDNWKFAIEGRASVYINRLLDGSTTMKGYTCEDILNGKYGEPGV

Target    MV-MVRTYPRHPFWEETNESKPMWTRSGRYENYRIEPEAIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPIT
7b04.1.B  AMLLFRTYPRHPFWEQVHESLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGPEATPYLPNAIVSTNPYIRPDDYGIPEN

Target    AQHHDDKTVRNIKLSWHEIKRHSNPLWEKGYQFYCVTPKTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIH
7b04.1.B  AEYWEDRTVRNIKKSWEETKKTKNFLWEKGYHFYCVTPKSRHTVHSQWAVTDWNFIWNNNFGDPYRMDKRMPGVGEHQIH

Target    INPQAAKDRGINDGDYVYVDGNPVDRPYRGWKPSDPYYKVARLMIRAKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPD
7b04.1.B  IHPQAARDLGIEDGDYVYVDANPADRPYEGWKPNDSFYKVSRLMLRAKYNPAYPYNCTMMKHSAWISSDKTVQAHETRP-

Target    GRAIAIDTGYQSNFRYGAQQSFTRNWLMPMHQTDSLPGKHAVAWKFKWGYQVDHHAINTVPKECLIRITKAEDGGIGARG
7b04.1.B  DGRALSPSGYQSSFRYGSQQSITRDWSMPMHQLDSLFHKAKIGMKFIFGFEADNHCINTVPKETLVKITKAENGGMGGKG

Target    PWEPVRTGFTPGQENEFMIKWLKGEHIKIKV
7b04.1.B  VWDPVKTGYTAGNENDFMKKFLNGELIKVD-

Model #03	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	1 x 6MO: MOLYBDENUM(VI) ION;	0.40	0.49 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
3ir5.1.A	20.97	monomer	0.00	HHblits	X-ray	2.30Å	0.31	2 - 1111	0.81	Respiratory nitrate reductase 1 alpha chain

Included Ligands

Ligand	Description
1 x 6MO	MOLYBDENUM(VI) ION

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
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    MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAF
3ir5.1.A  -FLDRFRYFKQKGETFADGH--------GQL-----------LNTNRDWEDGYRQRWQHDKIVRSTCGVNCTGSCSWKIY

Target    VRNGVVMRVEQNYDHQTYEDLYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGWK-QWMDDNA----P-----E
3ir5.1.A  VKNGLVTWETQQTDYPRT-----RPDLPNHEPRGCPRGASYSWYLYSANRLKYPMMRKRLMKMWREAKALHSDPVEAWAS

Target    -LTAETKRKYKFDSRFLDDMLRVSWDTAFTYAAKAMITIATRYSGEAGARRLREQGYAPEMIEMMKGAGTRCF-KHRAGM
3ir5.1.A  IIEDADKAKSFKQARGRGGFVRSSWQEVNELIAASNVYTIKNYGPDRVAGF--------------SPIPAMSMVSYASGA

Target    PVLGIIGKMGNTRMNGGINALLDTWIRKVSPDQAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFSKLNTSWGK
3ir5.1.A  RYLS---LIGGT--------------------------CLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGS

Target    NFVENKMPEAHWKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENM------HDIDFLKSFT
3ir5.1.A  NVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYT

Target    DAPILVRTD-------TLQYLDPRDVIADYKFPDFSKSYSGRIQSLKPEQIQRLGGMMVWDLNKKQVVPLHREQV-----
3ir5.1.A  DMPMLVMLEERDGYYAAGRMLRAADLVDALGQEN-----------------NPEWKTVAFNT-NGEMVAPNGSIGFRWGE

Target    --GWHYT----------------------------------------NSGIDAALTG---TYRVKLLNGREIDAMPIWQM
3ir5.1.A  KGKWNLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVYDL

Target    YM------------------VHFQDYDLDTVHQITRTPKDLIVRWARDSGTI-----KPAAIHNGEGTCHYFHQTANARG
3ir5.1.A  TLANYGLERGLNDVNCATSYDDVKAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHLDMNYRG

Target    AAMVLIITGNVGKFGTGQHTWAGNYKAGTWTATPWSGAGLSV----HT---GEDPF--------------N-ITLDPNAH
3ir5.1.A  LINMLIFCGCVGQSGGGWAHYVGQEKLRPQ--TGWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEELLSPMAD

Target    GKEIKTR---SYYYGEEVGYWNHG----DTALI---------VNTPKY-GRKVFTGKT--------HMPTPSKFRWVVNV
3ir5.1.A  KSRYTGHLIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLFIWRS

Target    NVVNNAKHHYD-MV------------------------------RNVDPNIECLITQDIEMTSDINHADIAFAANSWMEF
3ir5.1.A  NLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYEK

Target    TYPEMTVTVSNPWVQIWKGGIRPLYDTRNDLDTFAGVAAKLSDMTGD----K--------------------RMRDYFAM
3ir5.1.A  DDM--NTSDMHPFIHPLSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPIQHDSAAELAQPLDVKDWKKG

Target    V------------------YQNR---------------------------VDVYVQR-----------------------
3ir5.1.A  ECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAIDAA

Target    --MLDASSTFYGY----SADVMLKS------------EKGWMVMVR--------------------TYPRHPFWEETNES
3ir5.1.A  EMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYTNVHEL

Target    KPMWTRSGRYENYRIEPEAIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPITAQHHDDKTVRNIKLSWHEIK
3ir5.1.A  IPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSV-----------------------------------KEVIGQ-

Target    RHSNPLWEKGYQFYCVTPKTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIHINPQAAKDRGINDGDYVYVD
3ir5.1.A  ---KSNGNQEKALNFLTPHQKWGIHSTYSDNLLMLTLG---------------RGGPVVWLSEADAKDLGIADNDWIEVF

Target    GNPVDRPYRGWKPSDPYYKVARLMIRAKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPDGRAIAIDTGYQSNFRYGAQQ
3ir5.1.A  NS-----------------NGALTARAVVSQRVPAGMTMMYHAQERIVNL--------P--GSE------ITQQRGGIHN

Target    SFTRNWLMPMHQTDSLPGKHAVAWKFKWGYQVDHHAINTVPKECLIRITKAEDGGIGARGPWEPVRTGFTPGQENEFMIK
3ir5.1.A  SVTRITPKPTHMIGGYAHLA---------YGFNYYGTVGSNRDEFVVVRKMKNIDWL-----------------------

Target    WLKGEHIKIKV
3ir5.1.A  -----------

Model #02	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer (matching prediction)	None	0.37	0.48 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
1r27.4.A	20.78	homo-dimer	0.25	HHblits	X-ray	2.00Å	0.31	47 - 1111	0.81	Respiratory nitrate reductase 1 alpha chain

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
F3S.5	Binding site not conserved.	FE3-S4 CLUSTER
F3S.13	Binding site not conserved.	FE3-S4 CLUSTER
F3S.21	Binding site not conserved.	FE3-S4 CLUSTER
F3S.29	Binding site not conserved.	FE3-S4 CLUSTER
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
MGD.11	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.12	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.19	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.20	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.27	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.28	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.1	Not in contact with model.	MOLYBDENUM ATOM
MO.9	Binding site not conserved.	MOLYBDENUM ATOM
MO.17	Binding site not conserved.	MOLYBDENUM ATOM
MO.25	Binding site not conserved.	MOLYBDENUM ATOM
SF4.2	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
SF4.10	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.14	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.15	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.16	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.18	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.22	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.23	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.24	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.26	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.30	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.31	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.32	Binding site not conserved.	IRON/SULFUR CLUSTER

Target    MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAF
1r27.4.A  -FLDRFRYFKQKGETFADGHG--------QL-----------LNTNRDWEDGYRQRWQHDKIVRSTHGVNCTGSCSWKIY

Target    VRNGVVMRVEQNYDHQTYEDLYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGWK-QWMDDN----APEL----
1r27.4.A  VKNGLVTWETQQTDYPRT-----RPDLPNHEPRGCPRGASYSWYLYSANRLKYPMMRKRLMKMWREAKALHSDPVEAWAS

Target    --TAETKRKYKFDSRFLDDMLRVSWDTAFTYAAKAMITIATRYSGEAGARRLREQGYAPEMIEMMKGAGTRCF-KHRAGM
1r27.4.A  IIEDADKAKSFKQARGRGGFVRSSWQEVNELIAASNVYTIKNYGPDRVAGFS--------------PIPAMSMVSYASGA

Target    PVLGIIGKMGNTRMNGGINALLDTWIRKVSPDQAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFSKLNTSWGK
1r27.4.A  RYL---SLIGGT--------------------------CLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGS

Target    NFVENKMPEAHWKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENM------HDIDFLKSFT
1r27.4.A  NVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYT

Target    DAPILVRTDT-------LQYLDPRDVIADYKFPDFSKSYSGRIQSLKPEQIQRLGGMMVWDLNKKQVVPLHREQV-----
1r27.4.A  DMPMLVMLEERDGYYAAGRMLRAADLVDALGQEN-----------------NPEWKTVAFNT-NGEMVAPNGSIGFRWGE

Target    --GWHYTN----------------SGI-------D-------------AALT-------GTYRVKLLNGREIDAMPIWQM
1r27.4.A  KGKWNLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVYDL

Target    YM------------------VHFQDYDLDTVHQITRTPKDLIVRWARDSGTI-----KPAAIHNGEGTCHYFHQTANARG
1r27.4.A  TLANYGLERGLNDVNCATSYDDVKAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHLDMNYRG

Target    AAMVLIITGNVGKFGTGQHTWAGNYKA-GTWTATPWSGAGLSV----HT---GEDPF--------------N-ITLDPNA
1r27.4.A  LINMLIFCGCVGQSGGGWAHYVGQEKLRPQT---GWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEELLSPMA

Target    HGKEIKTR---SYYYGEEVGYWNH----GDTALI---------VNTPKYG-RKVFTGKT--------HMPTPSKFRWVVN
1r27.4.A  DKSRYTGHLIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLFIWR

Target    VNVVNNAKHHYD-MV------------------------------RNVDPNIECLITQDIEMTSDINHADIAFAANSWME
1r27.4.A  SNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYE

Target    FTYPEMTVTVSNPWVQIWKGGIRPLYDTRNDLDTFAGVAAKLSDMTGD----K--------------------RMRDYFA
1r27.4.A  KDDM--NTSDMHPFIHPLSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPIQHDSAAELAQPLDVKDWKK

Target    MV------------------YQN---------------------------RVDVYVQR----------------------
1r27.4.A  GECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAIDA

Target    ---MLDASSTFYGY----SADVMLKSE------------KGWMVMV--------------------RTYPRHPFWEETNE
1r27.4.A  AEMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYTNVHE

Target    SKPMWTRSGRYENYRIEPEAIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPITAQHHDDKTVRNIKLSWHEI
1r27.4.A  LIPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSV-------------KEVIG-----------------------

Target    KRHSNPLWEKGYQFYCVTPKTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIHINPQAAKDRGINDGDYVYV
1r27.4.A  ---QKSNGNQEKALNFLTPHQKWGIHSTYSDNLLMLTLG---------------RGGPVVWLSEADAKDLGIADNDWIEV

Target    DGNPVDRPYRGWKPSDPYYKVARLMIRAKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPDGRAIAIDTGYQSNFRYGAQ
1r27.4.A  FNS-----------------NGALTARAVVSQRVPAGMTMMYHAQERIVNL--------P--------GSEITQQRGGIH

Target    QSFTRNWLMPMHQTDSLPGKHAVAWKFKWGYQVDHHAINTVPKECLIRITKAEDGGIGARGPWEPVRTGFTPGQENEFMI
1r27.4.A  NSVTRITPKPTHMIGGYAHLA---------YGFNYYGTVGSNRDEFVVVRKMKNIDWL----------------------

Target    KWLKGEHIKIKV
1r27.4.A  ------------

Model #04	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.32	0.48 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
6sdv.1.A	20.13	monomer	0.00	HHblits	X-ray	1.90Å	0.30	42 - 747	0.53	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    MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAF
6sdv.1.A  MTVTRRHFLKLSAGAAVAGAFTGLGLSL---APTVA---RAEL--QK---------LQWAKQTTSICC-YCAVGCGLIVH

Target    VR---NGVVMRVEQNYDHQTYEDLYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGWKQWMDDNAPELTAETKR
6sdv.1.A  TAKDGQGRAVNVEGDPDHPI------------NEGSLCPKGASIFQLGENDQRGTQPLYRAPFS----------------

Target    KYKFDSRFLDDMLRVSWDTAFTYAAKAMITIATRYSGEAGARRLREQGYAPEMIEMMKGAGTRCFKHRAGMPVLGIIGKM
6sdv.1.A  ---------DTWKPVTWDFALTEIAKRIKKTRDASFTEKNAAGDLV--NRTEAIASFGSAAM------------------

Target    GNTRMNGGINALLDTWIRKVSPD-QAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFSKLNTSWGKNFVENKMP
6sdv.1.A  -----DNEECWAYGNILRSLGLVYIEHQARIU-----HSPTVPALAESFGRGAMTNHWNDLANSDCILIMGSNAAENHPI

Target    EAHWKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENMHDIDFLKSFTDAPILVRTDTLQYL
6sdv.1.A  AFKWVLRAKDKGATLIHVDPRFTRTSARCDVYAPIRSGADIPFLGGLIKYILDNKLYFTDYVREYTNASLIVGEKFSF--

Target    DPRDVIADYKFPDFSKSYSGRIQSLKPEQIQRLGGMMVWDLNKKQVVPLHREQVGWHYTNSGIDAALTGTYRVKLLNGRE
6sdv.1.A  --KDG----LFSGYD----A--------------ANKKYDKSM----------WAFELDA-------NG---VPKRDPAL

Target    IDAMPIWQMYMVHFQDYDLDTVHQITRTPKDLIVRWARDSGTI----KPAAIHNGEGTCHYFHQTANARGAAMVLIITGN
6sdv.1.A  KHPRCVINLLKKHYERYNLDKVAAITGTSKEQLQQVYKAYAATGKPDKAGTIMYAMGWTQHSVGVQNIRAMAMIQLLLGN

Target    VGKFGTGQHTWAGNYK-AGTWTATPWSGAGLSVHTGEDPFNIT-------LDPNAHGKEIKTRSYYYGEEVGYW------
6sdv.1.A  IGVAGGGVNALRGESNVQGSTDQ----GLLAHIWPGYNPVPNSKAATLELYNAATPQSKDPMSVNWWQNRPKYVASYLKA

Target    --NHGDT---ALIVN---T-----PKYGRKVFTGKTHMPTPSKFRWVVNVNVVNNAKHHYDMVRNVDPNIECLITQDIEM
6sdv.1.A  LYPDEEPAAAYDYLPRIDAGRKLTDYFWLNIFE--KMDKGEFKGLFAWGMNPACGGANA-NKNRKAMGKLEWLVNVNLFE

Target    TSDINH--------AD-----IAFAANSWMEFTYPEMTVTVSNPWVQIWKGGIRPLYDTRNDLDTFAGVAAKLSDMTGDK
6sdv.1.A  NETSSFWKGPGMNPAEIGTEVFFLPCCVSIEKEGS---VANSGRWMQWRYRGPKPYAETKPDGDIMLDMFKKVRE-----

Target    RMRDYFAMVYQNRVDVYVQRMLDASSTFYGYSADVMLKSEKGWMVMVRTYPRHPFWEETNESKPMWTRSGRYENYRIEPE
6sdv.1.A  --------------------------------------------------------------------------------

Target    AIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPITAQHHDDKTVRNIKLSWHEIKRHSNPLWEKGYQFYCVTP
6sdv.1.A  --------------------------------------------------------------------------------

Target    KTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIHINPQAAKDRGINDGDYVYVDGNPVDRPYRGWKPSDPYY
6sdv.1.A  --------------------------------------------------------------------------------

Target    KVARLMIRAKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPDGRAIAIDTGYQSNFRYGAQQSFTRNWLMPMHQTDSLPG
6sdv.1.A  --------------------------------------------------------------------------------

Target    KHAVAWKFKWGYQVDHHAINTVPKECLIRITKAEDGGIGARGPWEPVRTGFTPGQENEFMIKWLKGEHIKIKV
6sdv.1.A  -------------------------------------------------------------------------

Model #05	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer (matching prediction)	1 x MO: MOLYBDENUM ATOM;	0.21	0.44 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
1r27.4.A	27.20	homo-dimer	0.07	BLAST	X-ray	2.00Å	0.34	47 - 639	0.47	Respiratory nitrate reductase 1 alpha chain

Included Ligands

Ligand	Description
1 x MO	MOLYBDENUM ATOM

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
F3S.5	Binding site not conserved.	FE3-S4 CLUSTER
F3S.13	Binding site not conserved.	FE3-S4 CLUSTER
F3S.21	Binding site not conserved.	FE3-S4 CLUSTER
F3S.29	Binding site not conserved.	FE3-S4 CLUSTER
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
MGD.11	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.12	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.19	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.20	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.27	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.28	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.9	Binding site not conserved.	MOLYBDENUM ATOM
MO.17	Binding site not conserved.	MOLYBDENUM ATOM
MO.25	Binding site not conserved.	MOLYBDENUM ATOM
SF4.2	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
SF4.10	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.14	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.15	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.16	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.18	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.22	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.23	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.24	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.26	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.30	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.31	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.32	Binding site not conserved.	IRON/SULFUR CLUSTER

Target    MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAF
1r27.4.A  ---------------------------------------------NRDWEDGYRQRWQHDKIVRSTHGVNCTGSCSWKIY

Target    VRNGVVMRVEQNYDH-QTYEDLYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGW-KQWMDDNA---------P
1r27.4.A  VKNGLVTWETQQTDYPRTRPDLPN------HEPRGCPRGASYSWYLYSANRLKYPMMRKRLMKMWREAKALHSDPVEAWA

Target    ELTAETKRKYKF-DSRFLDDMLRVSWDTAFTYAAKAMITIATRYSGEAGARRLREQGYAPEMIEMMKGAGTRCFKHRAGM
1r27.4.A  SIIEDADKAKSFKQARGRGGFVRSSWQEVNELIAASNVYTIKNYGPD------RVAGFSP-------------------I

Target    PVLGIIGKMGNTRMNGGINALLDTWIRKVSPDQAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFSKLNTSWGK
1r27.4.A  PAMSMVSYASGARYLSLI-----------------GGTCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGS

Target    NFVENKMPEAHWKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENMHD------IDFLKSFT
1r27.4.A  NVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYT

Target    DAPILVRTD----------TLQYLDPRDVIADYKFPDFSK---SYSGRIQSLKPEQIQRLGGMMVWDLNKK---------
1r27.4.A  DMPMLVMLEERDGYYAAGRMLRAADLVDALGQENNPEWKTVAFNTNGEMVAPNGSIGFRWGEKGKWNLEQRDGKTGEETE

Target    -QVVPLHRE----QVGW---------HYTNSGIDAALTGTYRVKLLNGREIDAMPIWQMYMVHFQDYDLDT---------
1r27.4.A  LQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVYDLTLANYGLERGLNDVNCAT

Target    ------------VHQITRTPKDLIVRWARD-----SGTIKPAAIHNGEGTCHYFHQTANARGAAMVLIITGNVGKFGTGQ
1r27.4.A  SYDDVKAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHLDMNYRGLINMLIFCGCVGQSGGGW

Target    HTWAGNYKAGTWTATPWSGAGLSVHTGEDPFNITLDPNAHGKEIKTRSYYYGEEVGYWNHGDTALIVNTPKYGRKVFTGK
1r27.4.A  AHYVGQEK-------------LRPQTGWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEELLSPMADKSRYTG-

Target    THMPTPSKFRWVVNVNVVNNAKHHYDMVRNVDPNIECLITQDIEMTSDINHADIAFAANSWMEFTYPEMTVTVSNPWVQI
1r27.4.A  --------------------------------------------------------------------------------

Target    WKGGIRPLYDTRNDLDTFAGVAAKLSDMTGDKRMRDYFAMVYQNRVDVYVQRMLDASSTFYGYSADVMLKSEKGWMVMVR
1r27.4.A  --------------------------------------------------------------------------------

Target    TYPRHPFWEETNESKPMWTRSGRYENYRIEPEAIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPITAQHHDD
1r27.4.A  --------------------------------------------------------------------------------

Target    KTVRNIKLSWHEIKRHSNPLWEKGYQFYCVTPKTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIHINPQAA
1r27.4.A  --------------------------------------------------------------------------------

Target    KDRGINDGDYVYVDGNPVDRPYRGWKPSDPYYKVARLMIRAKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPDGRAIAI
1r27.4.A  --------------------------------------------------------------------------------

Target    DTGYQSNFRYGAQQSFTRNWLMPMHQTDSLPGKHAVAWKFKWGYQVDHHAINTVPKECLIRITKAEDGGIGARGPWEPVR
1r27.4.A  --------------------------------------------------------------------------------

Target    TGFTPGQENEFMIKWLKGEHIKIKV
1r27.4.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.

MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAFVRNGVVMRVEQNYDHQTYED
LYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGWKQWMDDNAPELTAETKRKYKFDSRFLDDMLRVSWDTAFTYAAKAMITIATRYSGEAGARR
LREQGYAPEMIEMMKGAGTRCFKHRAGMPVLGIIGKMGNTRMNGGINALLDTWIRKVSPDQAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFS
KLNTSWGKNFVENKMPEAHWKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENMHDIDFLKSFTDAPILVRTDTLQYLDPRD
VIADYKFPDFSKSYSGRIQSLKPEQIQRLGGMMVWDLNKKQVVPLHREQVGWHYTNSGIDAALTGTYRVKLLNGREIDAMPIWQMYMVHFQDYDLDTVHQ
ITRTPKDLIVRWARDSGTIKPAAIHNGEGTCHYFHQTANARGAAMVLIITGNVGKFGTGQHTWAGNYKAGTWTATPWSGAGLSVHTGEDPFNITLDPNAH
GKEIKTRSYYYGEEVGYWNHGDTALIVNTPKYGRKVFTGKTHMPTPSKFRWVVNVNVVNNAKHHYDMVRNVDPNIECLITQDIEMTSDINHADIAFAANS
WMEFTYPEMTVTVSNPWVQIWKGGIRPLYDTRNDLDTFAGVAAKLSDMTGDKRMRDYFAMVYQNRVDVYVQRMLDASSTFYGYSADVMLKSEKGWMVMVR
TYPRHPFWEETNESKPMWTRSGRYENYRIEPEAIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPITAQHHDDKTVRNIKLSWHEIKRHSNPL
WEKGYQFYCVTPKTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIHINPQAAKDRGINDGDYVYVDGNPVDRPYRGWKPSDPYYKVARLMIR
AKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPDGRAIAIDTGYQSNFRYGAQQSFTRNWLMPMHQTDSLPGKHAVAWKFKWGYQVDHHAINTVPKECLI
RITKAEDGGIGARGPWEPVRTGFTPGQENEFMIKWLKGEHIKIKV

Table T2:

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Coverage	Description
7b04.1.B	57.58	monomer	-	HHblits	X-ray	2.97Å	0.48	1.00	Nitrite oxidoreductase subunit A
7b04.1.B	58.37	monomer	-	BLAST	X-ray	2.97Å	0.49	1.00	Nitrite oxidoreductase subunit A
7b04.2.B	58.37	monomer	-	BLAST	X-ray	2.97Å	0.49	1.00	Nitrite oxidoreductase subunit A
7b04.2.B	57.58	monomer	-	HHblits	X-ray	2.97Å	0.48	1.00	Nitrite oxidoreductase subunit A
1r27.4.A	20.78	homo-dimer	0.25	HHblits	X-ray	2.00Å	0.31	0.81	Respiratory nitrate reductase 1 alpha chain
3ir5.1.A	20.97	monomer	-	HHblits	X-ray	2.30Å	0.31	0.81	Respiratory nitrate reductase 1 alpha chain
3egw.1.A	20.85	homo-dimer	0.17	HHblits	X-ray	1.90Å	0.31	0.78	Respiratory nitrate reductase 1 alpha chain
3ir7.1.A	20.86	monomer	-	HHblits	X-ray	2.50Å	0.31	0.81	Respiratory nitrate reductase 1 alpha chain
1q16.1.A	20.78	monomer	-	HHblits	X-ray	1.90Å	0.31	0.81	Respiratory nitrate reductase 1 alpha chain
3ir6.1.A	20.85	monomer	-	HHblits	X-ray	2.80Å	0.31	0.80	Respiratory nitrate reductase 1 alpha chain
2vpz.1.A	20.23	monomer	-	HHblits	X-ray	2.40Å	0.30	0.61	THIOSULFATE REDUCTASE
2vpx.1.D	20.23	monomer	-	HHblits	X-ray	3.10Å	0.30	0.61	THIOSULFATE REDUCTASE
2e7z.1.A	19.55	monomer	-	HHblits	X-ray	1.26Å	0.30	0.58	Acetylene hydratase Ahy
6sdv.1.A	20.13	monomer	-	HHblits	X-ray	1.90Å	0.30	0.53	Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit
8bqg.1.A	19.54	monomer	-	HHblits	X-ray	1.95Å	0.30	0.50	Formate dehydrogenase, alpha subunit, selenocysteine-containing
1r27.4.A	27.20	homo-dimer	0.07	BLAST	X-ray	2.00Å	0.34	0.47	Respiratory nitrate reductase 1 alpha chain
3ir5.1.A	27.39	monomer	-	BLAST	X-ray	2.30Å	0.34	0.47	Respiratory nitrate reductase 1 alpha chain
3ir7.1.A	27.20	monomer	-	BLAST	X-ray	2.50Å	0.34	0.47	Respiratory nitrate reductase 1 alpha chain
3egw.1.A	27.02	homo-dimer	0.07	BLAST	X-ray	1.90Å	0.34	0.47	Respiratory nitrate reductase 1 alpha chain
1q16.1.A	27.20	monomer	-	BLAST	X-ray	1.90Å	0.34	0.47	Respiratory nitrate reductase 1 alpha chain
3ir6.1.A	27.20	monomer	-	BLAST	X-ray	2.80Å	0.34	0.47	Respiratory nitrate reductase 1 alpha chain
6q8o.1.C	14.74	monomer	-	HHblits	X-ray	3.61Å	0.26	0.44	NADH-quinone oxidoreductase subunit 3
6ziy.1.C	14.74	monomer	-	HHblits	EM	NA	0.26	0.44	NADH-quinone oxidoreductase subunit 3
6zjl.1.C	14.74	monomer	-	HHblits	EM	NA	0.26	0.44	NADH-quinone oxidoreductase subunit 3
6zjn.1.C	14.74	monomer	-	HHblits	EM	NA	0.26	0.44	NADH-quinone oxidoreductase subunit 3
3m9s.1.C	14.74	monomer	-	HHblits	X-ray	4.50Å	0.26	0.44	NADH-quinone oxidoreductase subunit 3
6zjy.1.C	14.74	monomer	-	HHblits	EM	NA	0.26	0.44	NADH-quinone oxidoreductase subunit 3
2fug.2.C	14.74	monomer	-	HHblits	X-ray	3.30Å	0.26	0.44	NADH-quinone oxidoreductase chain 3
6zk9.1.C	11.75	monomer	-	HHblits	EM	NA	0.25	0.33	NADH:ubiquinone oxidoreductase core subunit S1
7zd6.1.4	11.75	monomer	-	HHblits	EM	NA	0.25	0.33	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6qcf.1.C	11.78	monomer	-	HHblits	EM	NA	0.25	0.33	NADH:ubiquinone oxidoreductase core subunit S1
7qsd.1.G	11.75	monomer	-	HHblits	EM	NA	0.25	0.33	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6qc5.1.C	11.78	monomer	-	HHblits	EM	NA	0.25	0.33	NADH:ubiquinone oxidoreductase core subunit S1
5o31.1.8	12.01	monomer	-	HHblits	EM	4.13Å	0.25	0.33	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7dgr.10.A	12.01	monomer	-	HHblits	EM	NA	0.25	0.33	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6sdr.1.A	26.60	monomer	-	BLAST	X-ray	2.10Å	0.35	0.08	Formate dehydrogenase, alpha subunit, selenocysteine-containing
8bqg.1.A	26.60	monomer	-	BLAST	X-ray	1.95Å	0.35	0.08	Formate dehydrogenase, alpha subunit, selenocysteine-containing
6sdv.1.A	26.60	monomer	-	BLAST	X-ray	1.90Å	0.35	0.08	Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit
2vpx.1.D	32.20	monomer	-	BLAST	X-ray	3.10Å	0.40	0.05	THIOSULFATE REDUCTASE
2e7z.1.A	37.93	monomer	-	BLAST	X-ray	1.26Å	0.41	0.05	Acetylene hydratase Ahy
2vpz.1.A	32.20	monomer	-	BLAST	X-ray	2.40Å	0.40	0.05	THIOSULFATE REDUCTASE
1m2j.1.A	24.53	monomer	-	HHblits	X-ray	1.70Å	0.32	0.05	Silent Information Regulator 2
3k35.1.A	20.37	monomer	-	HHblits	X-ray	2.00Å	0.30	0.05	NAD-dependent deacetylase sirtuin-6
1ici.1.A	23.64	monomer	-	HHblits	X-ray	2.10Å	0.31	0.05	TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
1m2h.1.A	24.53	monomer	-	HHblits	X-ray	1.80Å	0.32	0.05	Silent Information Regulator 2
4twi.1.A	24.07	monomer	-	HHblits	X-ray	1.79Å	0.32	0.05	NAD-dependent protein deacylase 1
1m2k.1.A	24.53	monomer	-	HHblits	X-ray	1.47Å	0.32	0.05	Silent Information Regulator 2
1m2g.1.A	24.53	monomer	-	HHblits	X-ray	1.70Å	0.32	0.05	Silent Information Regulator 2
6xvg.3.A	20.37	monomer	-	HHblits	X-ray	2.10Å	0.30	0.05	NAD-dependent protein deacetylase sirtuin-6
3riy.2.A	20.00	monomer	-	HHblits	X-ray	1.55Å	0.29	0.05	NAD-dependent deacetylase sirtuin-5

The table above shows the top 50 filtered templates. A further 346 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, 1jeo.1.A, 1kb9.1.E, 1kqf.1.A, 1l0l.1.E, 1l0n.1.E, 1m2n.1.A, 1m2n.1.B, 1m3s.1.A, 1m3s.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, 1tk9.1.A, 1tmo.1.A, 1vf5.1.D, 1vf5.1.L, 1vim.1.A, 1vim.1.D, 1viv.1.A, 1wlf.1.A, 1x94.1.A, 1x94.1.B, 1yc5.1.A, 1zrt.1.C, 1zrt.1.F, 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, 2xbl.1.A, 2ybb.1.b, 3cf4.1.B, 3cwb.1.E, 3egw.1.A, 3etn.1.A, 3fxa.1.A, 3h1h.1.E, 3h1h.1.O, 3h1i.1.E, 3hu2.1.A, 3ir5.1.A, 3ir6.1.A, 3ir7.1.A, 3jr3.1.A, 3jwp.1.A, 3l75.1.E, 3l75.1.O, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3pki.1.A, 3qc8.1.A, 3qq7.1.A, 3qq8.1.A, 3qwz.1.A, 3sho.1.A, 3sho.1.C, 3tiw.1.A, 3tiw.2.A, 3u31.1.A, 3zg6.1.A, 4aay.1.A, 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, 4kdi.1.A, 4kdi.2.A, 4kdl.1.A, 4ogq.1.L, 4pv1.1.L, 4rv0.1.A, 4twj.1.A, 4u3f.1.E, 4utn.1.A, 4utn.2.A, 4v4c.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, 5g4g.1.A, 5glf.1.A, 5glf.2.A, 5glf.3.A, 5glf.4.A, 5gpn.24.A, 5kkz.1.C, 5kli.1.C, 5klv.1.P, 5ltz.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, 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, 6ljk.1.A, 6ljm.1.A, 6lod.1.B, 6nhg.1.E, 6nin.1.C, 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, 6xkt.1.E, 6xkz.1.F, 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, 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, 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 #03

Included Ligands

Excluded ligands

Model #02

Excluded ligands

Model #04

Excluded ligands

Model #05

Included Ligands

Excluded ligands

Materials and Methods

Template Search

Template Selection

Model Building

Model Quality Estimation

Ligand Modelling

Oligomeric State Conservation

References

Table T1:

Table T2: