21_Jan_SF_Bin67_scaffold_32672_c1:3-2330_1

SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "21_Jan_SF_Bin67_scaffold_32672_c1:3-2330_1" submitted to SWISS-MODEL workspace on March 29, 2023, 6:30 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 282 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	None	0.81	0.78 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
7b04.1.B	53.57	monomer	0.00	HHblits	X-ray	2.97Å	0.46	1 - 772	1.00	Nitrite oxidoreductase subunit A

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
MO.7	Binding site not conserved.	MOLYBDENUM ATOM
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    RPFLERFTDMPLLVRLDTLQRLRADEVFADYSSDLDVDGPSFTLHGMTEEQHERNGDRVVFDDASGALRAINREDVGDRL
7b04.1.B  ADYVKKFTDFPLLIRTDTLKRVSPKDIIPNYKLQDISDGPSYHIQGLKDEQREIIGDFVVWDAKSKGPKAITRDDVGETL

Target    DDKGIDPALDYQGTVTLVDGSTVEVMSVLSMYREHLADYDIDSVVDMTGAPRNLIEQLLDDMTTLSPVAFHVGEGVNHYF
7b04.1.B  VKKGIDPVLEGSFKLKTIDGKEIEVMTLLEMYKIHLRDYDIDSVVSMTNSPKDLIERLAKDIATIKPVAIHYGEGVNHYF

Target    HATLHNRATYLVGMLLGSVGVSGGGVSTWAGNYKGGVFQAAPWFGPGVGGFVNEDPFHPLTDPSARYSAETARHLVHGED
7b04.1.B  HATLMNRSYYLPVMLTGNVGYFGSGSHTWAGNYKAGNFQASKWSGPGFYGWVAEDVFKPNLDPYASAKDLNIKGRALDEE

Target    TSYWGFGDRPLVVDTPEDGRKVFTGTTHMPTPTKALWYNNANLINQAKWHYELVKNVNPKVDLIVDQQIEWTGSAEFADI
7b04.1.B  VAYWNHSERPLIVNTPKYGRKVFTGKTHMPSPTKVLWFTNVNLINNAKHVYQMLKNVNPNIEQIMSTDIEITGSIEYADF

Target    VLPANSWMEAETWEMGASCSNPFLQVWK-GGIEPLNDTRDDIAIFAGVANALTELTGDERFSQAFMF--ADRPEVYLDRV
7b04.1.B  AFPANSWVEFQEFEITNSCSNPFIQIWGKTGITPVYESKDDVKILAGMASKLGELLRDKRFEDNWKFAIEGRASVYINRL

Target    LAGSFTTEGYTVEDLTAGRYGPPGGALMQYRSYPRIPFKEQIEDSLPFYTDTGRMHGYVDIPEAIEYGENLIVHREAVEA
7b04.1.B  LDGSTTMKGYTCEDILNGKYGEPGVAMLLFRTYPRHPFWEQVHESLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGPEA

Target    TPYLPNVIVSTSPYLRPRDYGIAPEELDGDARSVRNIMMSWAEVKETENPLFAAGYNYLCLTPKSRHAVHSSWAVTDWHW
7b04.1.B  TPYLPNAIVSTNPYIRPDDYGIPENAEYWEDRTVRNIKKSWEETKKTKNFLWEKGYHFYCVTPKSRHTVHSQWAVTDWNF

Target    LWSSSFSDPYRVETRAPGVGEPAIHLNPDDARSLGIRNGDYVWVDSNPKDRPYRDADVDESFLDVARLLVRVTYNPAYPP
7b04.1.B  IWNNNFGDPYRMDKRMPGVGEHQIHIHPQAARDLGIEDGDYVYVDANPADRPYEGWKPNDSFYKVSRLMLRAKYNPAYPY

Target    GVTMLKHAFYMATPRTFRAAQERSDGRALAETTGYQSSFRSGSHQSITRGWAPPMHQTDSLFHKRAGVFGFTYGFDVDNH
7b04.1.B  NCTMMKHSAWISSDKTVQAHETRPDGRALSP-SGYQSSFRYGSQQSITRDWSMPMHQLDSLFHKAKIGMKFIFGFEADNH

Target    AINTVPKETVVRITKAEDGGVGGSGAWTRGRPGSMPGDEDDAMQAYLAGELTVVRRT
7b04.1.B  CINTVPKETLVKITKAENGGMGGKGVWDPVKTGYTAGNENDFMKKFLNGELIKVD--

Model #02	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.40	0.45 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
3ir7.1.A	22.74	monomer	0.00	HHblits	X-ray	2.50Å	0.31	1 - 739	0.80	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    RPFLERFTDMPLLVRLD-------TLQRLRADEVFADYSSDLDVDGPSFTLHGMTEEQHERNGDRVVFDDASGALRAINR
3ir7.1.A  TDYVRRYTDMPMLVMLEERDGYYAAGRMLRAADLVDAL-------GQ----------ENNPEWKTVAFNT-NGEMVAPNG

Target    EDVGD--------------------RLD---DK------------------------GIDPALDY---QGTVTLVDGSTV
3ir7.1.A  SIGFRWGEKGKWNLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTA

Target    EVMSVLSMYR------------------EHLADYDIDSVVDMTGAPRNLIEQLLDDMTTL-----SPVAFHVGEGVNHYF
3ir7.1.A  LVTTVYDLTLANYGLERGLNDVNCATSYDDVKAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWY

Target    HATLHNRATYLVGMLLGSVGVSGGGVSTWAGNYKGGV---FQ----AAPWFGPGVGGFVNEDPFHPLTDPSARYSA----
3ir7.1.A  HLDMNYRGLINMLIFCGCVGQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQRPA--RHMNSTSYFYNHSSQWRYETVTAE

Target    --------------ETAR----HLVHGEDTSYWGFGDRPL----------------VVDTPEDGRKVF--TGTTHMPTPT
3ir7.1.A  ELLSPMADKSRYTGHLIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHP

Target    KALWYNNANLINQAKWHYEL-------------------------------VKNVNPKVDLIVDQQIEWTGSAEFADIVL
3ir7.1.A  RNLFIWRSNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIIL

Target    PANSWMEAETWEMGASCSNPFLQVWKGGIEPLNDTRDDIAIFAGVANALTELTGDE---R---FSQAFMFADRP------
3ir7.1.A  PTATWYEKDDMN--TSDMHPFIHPLSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPI-QHDSAAELAQP

Target    ---EVY---------------------------------------------------------LDRV-------------
3ir7.1.A  LDVKDWKKGECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQP

Target    ------------LAGSFTTEG----YTVEDLTAGRYG-----PP--GGALMQYR---------------------SYPRI
3ir7.1.A  MLNTAIDAAEMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYN

Target    PFKEQIEDSLPFYTDTGRMHGYVDIPEAIEYGENLIVHREAVEATPYLPNVIVSTSPYLRPRDYGIAPEELDGDARSVRN
3ir7.1.A  AGYTNVHELIPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSV-KE------------------------------

Target    IMMSWAEVKETENPLFAAGYNYLCLTPKSRHAVHSSWAVTDWHWLWSSSFSDPYRVETRAPGVGEPAIHLNPDDARSLGI
3ir7.1.A  ----VI---G-QKSNGNQEKALNFLTPHQKWGIHSTYSDNLLM------------LTL---GRGGPVVWLSEADAKDLGI

Target    RNGDYVWVDSNPKDRPYRDADVDESFLDVARLLVRVTYNPAYPPGVTMLKHAFYMATPRTFRAAQERSDGRALAETTGYQ
3ir7.1.A  ADNDWIEVFNS-----------------NGALTARAVVSQRVPAGMTMMYHAQERIVN------------LPGSEI----

Target    SSFRSGSHQSITRGWAPPMHQTDSLFHKRAGVFGFTYGFDVDNHAINTVPKETVVRITKAEDGGVGGSGAWTRGRPGSMP
3ir7.1.A  TQQRGGIHNSVTRITPKPTHMI-------GGYAHLAYGFNYYGT--VGSNRDEFVVVRKMKNIDWL--------------

Target    GDEDDAMQAYLAGELTVVRRT
3ir7.1.A  ---------------------

Model #03	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.21	0.37 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
2ivf.1.A	32.76	monomer	0.00	BLAST	X-ray	1.88Å	0.36	1 - 473	0.53	ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
ACT.2	Not biologically relevant.	ACETATE ION
ACT.7	Not biologically relevant.	ACETATE ION
F3S.15	Binding site not conserved.	FE3-S4 CLUSTER
GOL.3	Not biologically relevant.	GLYCEROL
GOL.4	Not biologically relevant.	GLYCEROL
GOL.5	Not biologically relevant.	GLYCEROL
GOL.6	Not biologically relevant.	GLYCEROL
GOL.12	Not biologically relevant.	GLYCEROL
GOL.14	Not biologically relevant.	GLYCEROL
GOL.19	Not biologically relevant.	GLYCEROL
GOL.20	Not biologically relevant.	GLYCEROL
HEM.21	Binding site not conserved.	PROTOPORPHYRIN IX CONTAINING FE
MD1.11	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
MES.1	Binding site not conserved.	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
MGD.10	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
PO4.13	Not biologically relevant.	PHOSPHATE ION
SF4.8	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.16	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.17	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.18	Binding site not conserved.	IRON/SULFUR CLUSTER

Target    RPFLERFTDMPLLVRLDTLQRLRADEVFADYSSDLDVDGPSFTLHGMTEEQHERNGDRVVFDDASGALRAINREDVGDRL
2ivf.1.A  RQFVCEQTDLPLLVRMDTGKFLSAE----------DVDG------GEAKQFY-------FFDEKAGSVRKASRGTL--KL

Target    DDKGIDPALDYQGTVTLVDGSTVEVMSVLSMYREHLADYDIDSVVDMTGAPRNLIEQLLDDMTTLSPVAFHVGEGVNHYF
2ivf.1.A  D---FMPALEGTFSARLKNGKTIQVRTVFEGLREHLKDYTPEKASAKCGVPVSLIRELGRKVAKKRTCSY-IGFSSAKSY

Target    HATLHNRATYLVGMLLGSVGVSGGGVSTWAGNYKGGVFQAAPWFGPGVGGFV------NEDPFHPLTDPSARYSAETARH
2ivf.1.A  HGDLMERSLFLAMAL--------------SGN----------WGKPGTGAFAWAYSDDNMVYLGVMSKPTAQGGMDELHQ

Target    LVHGEDTSYWGFGDRPLVVD---TPEDGR----KVFTGTTHMPTPTKALWYNNA--NLINQAKW----------------
2ivf.1.A  MAE-------GFNKRTLEADPTSTDEMGNIEFMKVVTSAVGLVPPAMWLYYHVGYDQLWNNKAWTDPALKKSFGAYLDEA

Target    ---------HYELVKNVNPKVDLIVDQ---------------------------QIEWTGSAEFADIVLPANSWMEAETW
2ivf.1.A  KEKGWWTNDHIRPAPDKTPQVYMLLSQNPMRRKRSGAKMFPDVLFPKLKMIFALETRMSSSAMYADIVLPCAWYYEKH--

Target    EMGASCS-NPFLQVWKGGIEPLNDTR---DDIAIFA------GVANALTELTG--------DERFSQAFMFAD-------
2ivf.1.A  EMTTPCSGNPFFTFVDRSVAPPGECREEWDAIALILKKVGERAAARGLTEFNDHNGRKRRYDELYKKFTMDGHLLTNEDC

Target    -RPEVYLDR---VLAGSFTTEGYTVEDLTAGRYGPPGGALMQYR-------SYPRIPFKEQIEDSLPFYTDTGRMHGYVD
2ivf.1.A  LKEMVDINRAVGVFAKDYTYEKFKKEGQT--RFLSMGTGVSRYAHANEVDVTKPIYPMRWHFDDKKVFPTHTRRAQFYLD

Target    IPEAIEYGENLIVHREAVEATPYLPNVIVSTSPYLRPRDYGIAPEELDGDARSVRNIMMSWAEVKETENPLFAAGYNYLC
2ivf.1.A  HDWYLEAGESLPTHKD----------------------------------------------------------------

Target    LTPKSRHAVHSSWAVTDWHWLWSSSFSDPYRVETRAPGVGEPAIHLNPDDARSLGIRNGDYVWVDSNPKDRPYRDADVDE
2ivf.1.A  --------------------------------------------------------------------------------

Target    SFLDVARLLVRVTYNPAYPPGVTMLKHAFYMATPRTFRAAQERSDGRALAETTGYQSSFRSGSHQSITRGWAPPMHQTDS
2ivf.1.A  --------------------------------------------------------------------------------

Target    LFHKRAGVFGFTYGFDVDNHAINTVPKETVVRITKAEDGGVGGSGAWTRGRPGSMPGDEDDAMQAYLAGELTVVRRT
2ivf.1.A  -----------------------------------------------------------------------------

Model #04	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.12	0.33 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
2fug.2.C	16.58	monomer	0.00	HHblits	X-ray	3.30Å	0.27	296 - 649	0.25	NADH-quinone oxidoreductase chain 3

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
FES.2	Binding site not conserved.	FE2/S2 (INORGANIC) CLUSTER
FES.6	Binding site not conserved.	FE2/S2 (INORGANIC) CLUSTER
FMN.10	Binding site not conserved.	FLAVIN MONONUCLEOTIDE
SF4.1	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.3	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.4	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.5	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
SF4.9	Binding site not conserved.	IRON/SULFUR CLUSTER

Target    RPFLERFTDMPLLVRLDTLQRLRADEVFADYSSDLDVDGPSFTLHGMTEEQHERNGDRVVFDDASGALRAINREDVGDRL
2fug.2.C  --------------------------------------------------------------------------------

Target    DDKGIDPALDYQGTVTLVDGSTVEVMSVLSMYREHLADYDIDSVVDMTGAPRNLIEQLLDDMTTLSPVAFHVGEGVNHYF
2fug.2.C  --------------------------------------------------------------------------------

Target    HATLHNRATYLVGMLLGSVGVSGGGVSTWAGNYKGGVFQAAPWFGPGVGGFVNEDPFHPLTDPSARYSAETARHLVHGED
2fug.2.C  --------------------------------------------------------------------------------

Target    TSYWGFGDRPLVVDTPEDGRKVFTGTTHMPTPTKALWYNNANLINQAKWHYELVKNVNPKVDLIVDQQIEWTGSA-EFAD
2fug.2.C  -------------------------------------------------------EALKGKRFVVMHLSHLHPLAERYAH

Target    IVLPANSWMEAETWEMGASCSNPFLQVWKGGIEPLNDTRDDIAIFAGVANALTELTGDERFSQAFMFADRPEVYLDRVLA
2fug.2.C  VVLPAPTFYEKRGH---LVNLEGRVLPLSPAPIENGEAEGALQVLALLAEALGVR-------P--PFR-LHLEA------

Target    GSFTTEGYTVEDLTAGRYGPPGGALMQYRSYPRIPFKEQIEDSLPFYTDTGRMHGYVDIPEAIEYGENLIVHREAVEATP
2fug.2.C  ---------QKALKA----------------------------RKVPEAMGRLSFRLKELR------------------P

Target    YLPNVIVSTSPYLRPRDYGIAPEELDGDARSVRNIMMSWAEVKETENPLFAAGYNYLCLTPKSRHAVHSSWAVTDWHWLW
2fug.2.C  -------------------------------------------------KERKGAFYLRPTMW--KAHQ---AVGK--A-

Target    SSSFSDPYRVETRAPGVGEPAIHLNPDDARSLGIRNGDYVWVDSNPKDRPYRDADVDESFLDVARLLVRVTYNPAYPPGV
2fug.2.C  ---------Q-----EAARAELWAHPETARAEALPEGAQVAVETP-----------------FGRVEARVVHREDVPKGH

Target    TMLKHAFYMATPRTFRAAQERSDGRALAETTGYQSSFRSGSHQSITRGWAPPMHQTDSLFHKRAGVFGFTYGFDVDNHAI
2fug.2.C  LYLSALGPAAG---------------------------------------------------------------------

Target    NTVPKETVVRITKAEDGGVGGSGAWTRGRPGSMPGDEDDAMQAYLAGELTVVRRT
2fug.2.C  -------------------------------------------------------

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.

RPFLERFTDMPLLVRLDTLQRLRADEVFADYSSDLDVDGPSFTLHGMTEEQHERNGDRVVFDDASGALRAINREDVGDRLDDKGIDPALDYQGTVTLVDG
STVEVMSVLSMYREHLADYDIDSVVDMTGAPRNLIEQLLDDMTTLSPVAFHVGEGVNHYFHATLHNRATYLVGMLLGSVGVSGGGVSTWAGNYKGGVFQA
APWFGPGVGGFVNEDPFHPLTDPSARYSAETARHLVHGEDTSYWGFGDRPLVVDTPEDGRKVFTGTTHMPTPTKALWYNNANLINQAKWHYELVKNVNPK
VDLIVDQQIEWTGSAEFADIVLPANSWMEAETWEMGASCSNPFLQVWKGGIEPLNDTRDDIAIFAGVANALTELTGDERFSQAFMFADRPEVYLDRVLAG
SFTTEGYTVEDLTAGRYGPPGGALMQYRSYPRIPFKEQIEDSLPFYTDTGRMHGYVDIPEAIEYGENLIVHREAVEATPYLPNVIVSTSPYLRPRDYGIA
PEELDGDARSVRNIMMSWAEVKETENPLFAAGYNYLCLTPKSRHAVHSSWAVTDWHWLWSSSFSDPYRVETRAPGVGEPAIHLNPDDARSLGIRNGDYVW
VDSNPKDRPYRDADVDESFLDVARLLVRVTYNPAYPPGVTMLKHAFYMATPRTFRAAQERSDGRALAETTGYQSSFRSGSHQSITRGWAPPMHQTDSLFH
KRAGVFGFTYGFDVDNHAINTVPKETVVRITKAEDGGVGGSGAWTRGRPGSMPGDEDDAMQAYLAGELTVVRRT

Table T2:

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Coverage	Description
7b04.1.B	53.57	monomer	-	HHblits	X-ray	2.97Å	0.46	1.00	Nitrite oxidoreductase subunit A
7b04.1.B	54.04	monomer	-	BLAST	X-ray	2.97Å	0.46	0.99	Nitrite oxidoreductase subunit A
7b04.2.B	53.57	monomer	-	HHblits	X-ray	2.97Å	0.46	1.00	Nitrite oxidoreductase subunit A
7b04.2.B	54.04	monomer	-	BLAST	X-ray	2.97Å	0.46	0.99	Nitrite oxidoreductase subunit A
3ir7.1.A	22.74	monomer	-	HHblits	X-ray	2.50Å	0.31	0.80	Respiratory nitrate reductase 1 alpha chain
3egw.1.A	22.85	homo-dimer	0.06	HHblits	X-ray	1.90Å	0.31	0.80	Respiratory nitrate reductase 1 alpha chain
3ir6.1.A	23.05	monomer	-	HHblits	X-ray	2.80Å	0.32	0.80	Respiratory nitrate reductase 1 alpha chain
1q16.1.A	22.74	monomer	-	HHblits	X-ray	1.90Å	0.31	0.80	Respiratory nitrate reductase 1 alpha chain
3ir5.1.A	22.58	monomer	-	HHblits	X-ray	2.30Å	0.31	0.80	Respiratory nitrate reductase 1 alpha chain
1r27.4.A	22.74	homo-dimer	-	HHblits	X-ray	2.00Å	0.31	0.80	Respiratory nitrate reductase 1 alpha chain
1dms.1.A	21.85	monomer	-	HHblits	X-ray	1.88Å	0.30	0.57	DMSO REDUCTASE
1e60.1.A	21.95	monomer	-	HHblits	X-ray	2.00Å	0.30	0.57	Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e5v.2.A	21.95	monomer	-	HHblits	X-ray	2.40Å	0.30	0.57	Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e18.1.A	22.12	monomer	-	HHblits	X-ray	2.00Å	0.30	0.57	DMSO REDUCTASE.
4dmr.1.A	21.80	monomer	-	HHblits	X-ray	1.90Å	0.30	0.57	DMSO REDUCTASE
2ivf.1.A	32.76	monomer	-	BLAST	X-ray	1.88Å	0.36	0.53	ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
6q8o.1.C	16.58	monomer	-	HHblits	X-ray	3.61Å	0.27	0.25	NADH-quinone oxidoreductase subunit 3
6zjl.1.C	16.58	monomer	-	HHblits	EM	NA	0.27	0.25	NADH-quinone oxidoreductase subunit 3
6ziy.1.C	16.58	monomer	-	HHblits	EM	NA	0.27	0.25	NADH-quinone oxidoreductase subunit 3
6zjn.1.C	16.58	monomer	-	HHblits	EM	NA	0.27	0.25	NADH-quinone oxidoreductase subunit 3
3m9s.1.C	16.58	monomer	-	HHblits	X-ray	4.50Å	0.27	0.25	NADH-quinone oxidoreductase subunit 3
6zjy.1.C	16.58	monomer	-	HHblits	EM	NA	0.27	0.25	NADH-quinone oxidoreductase subunit 3
2fug.2.C	16.58	monomer	-	HHblits	X-ray	3.30Å	0.27	0.25	NADH-quinone oxidoreductase chain 3
6zk9.1.C	16.18	monomer	-	HHblits	EM	NA	0.27	0.22	NADH:ubiquinone oxidoreductase core subunit S1
7zd6.1.4	16.18	monomer	-	HHblits	EM	NA	0.27	0.22	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7dgr.10.A	16.18	monomer	-	HHblits	EM	NA	0.27	0.22	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6qcf.1.C	15.61	monomer	-	HHblits	EM	NA	0.27	0.22	NADH:ubiquinone oxidoreductase core subunit S1
6qc5.1.C	15.61	monomer	-	HHblits	EM	NA	0.27	0.22	NADH:ubiquinone oxidoreductase core subunit S1
5o31.1.8	16.18	monomer	-	HHblits	EM	4.13Å	0.27	0.22	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
2pjh.1.B	11.54	monomer	-	HHblits	NMR	NA	0.26	0.07	Transitional endoplasmic reticulum ATPase
5x4l.2.A	11.32	monomer	-	HHblits	X-ray	2.40Å	0.26	0.07	Transitional endoplasmic reticulum ATPase
3ir5.1.A	12.96	monomer	-	HHblits	X-ray	2.30Å	0.25	0.07	Respiratory nitrate reductase 1 alpha chain
5x4l.1.A	11.32	monomer	-	HHblits	X-ray	2.40Å	0.26	0.07	Transitional endoplasmic reticulum ATPase
4kdl.1.A	11.54	monomer	-	HHblits	X-ray	1.81Å	0.26	0.07	Transitional endoplasmic reticulum ATPase
5b6c.1.A	11.54	monomer	-	HHblits	X-ray	1.55Å	0.26	0.07	Transitional endoplasmic reticulum ATPase
3qc8.1.A	11.76	monomer	-	HHblits	X-ray	2.20Å	0.26	0.07	Transitional endoplasmic reticulum ATPase
4kdi.1.A	11.54	monomer	-	HHblits	X-ray	1.86Å	0.26	0.07	Transitional endoplasmic reticulum ATPase
3ir6.1.A	12.96	monomer	-	HHblits	X-ray	2.80Å	0.25	0.07	Respiratory nitrate reductase 1 alpha chain
4kdi.2.A	11.54	monomer	-	HHblits	X-ray	1.86Å	0.26	0.07	Transitional endoplasmic reticulum ATPase
1r27.4.A	12.96	monomer	-	HHblits	X-ray	2.00Å	0.25	0.07	Respiratory nitrate reductase 1 alpha chain
3ir7.1.A	13.21	monomer	-	HHblits	X-ray	2.50Å	0.25	0.07	Respiratory nitrate reductase 1 alpha chain
3egw.1.A	12.96	monomer	-	HHblits	X-ray	1.90Å	0.25	0.07	Respiratory nitrate reductase 1 alpha chain
1q16.1.A	12.96	monomer	-	HHblits	X-ray	1.90Å	0.25	0.07	Respiratory nitrate reductase 1 alpha chain
1e60.1.A	14.55	monomer	-	HHblits	X-ray	2.00Å	0.27	0.07	Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e18.1.A	14.55	monomer	-	HHblits	X-ray	2.00Å	0.27	0.07	DMSO REDUCTASE.
1e5v.2.A	14.55	monomer	-	HHblits	X-ray	2.40Å	0.27	0.07	Dimethyl sulfoxide/trimethylamine N-oxide reductase
4dmr.1.A	14.81	monomer	-	HHblits	X-ray	1.90Å	0.27	0.07	DMSO REDUCTASE
1dms.1.A	14.81	monomer	-	HHblits	X-ray	1.88Å	0.27	0.07	DMSO REDUCTASE
5cup.1.A	46.15	monomer	-	HHblits	X-ray	2.10Å	0.43	0.03	Phosphate propanoyltransferase
5cuo.1.A	46.15	monomer	-	HHblits	X-ray	1.54Å	0.43	0.03	Phosphate propanoyltransferase

The table above shows the top 50 filtered templates. A further 179 templates were found which were considered to be less suitable for modelling than the filtered list.
1aa6.1.A, 1cz4.1.A, 1cz5.1.A, 1eu1.1.A, 1fdo.1.A, 1g8j.1.A, 1g8k.1.A, 1h0h.1.A, 1j75.1.A, 1kqf.1.A, 1ogy.1.A, 1tmo.1.A, 1uhd.1.B, 1uhe.1.B, 1wlf.1.A, 2d9r.1.A, 2e7z.1.A, 2heo.1.A, 2heo.1.B, 2iv2.1.A, 2ivf.1.A, 2ki8.1.A, 2kz3.1.A, 2l1p.1.A, 2lnb.1.A, 2mrn.1.A, 2mru.1.A, 2mru.1.B, 2nya.1.A, 2o3f.1.A, 2v3v.1.A, 2v45.1.A, 2vpx.1.D, 2vpz.1.A, 2xvc.1.A, 3hu1.1.A, 3hu2.1.A, 3iwf.1.A, 3nzl.1.A, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3plx.1.B, 3qq7.1.A, 3qq8.1.A, 3qwz.1.A, 3tiw.1.A, 3tiw.2.A, 4aay.1.A, 4ga5.1.A, 4ga6.1.A, 4rv0.1.A, 4v4c.1.A, 4ydd.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, 5itm.1.A, 5itm.1.B, 5itm.1.E, 5nqd.1.A, 5t5i.1.B, 5t5i.1.D, 5xtb.1.L, 6btm.1.B, 6cz7.1.A, 6f0k.1.B, 6f49.1.A, 6g72.1.G, 6gcs.1.A, 6hd3.1.A, 6lod.1.B, 6rfq.1.A, 6rfs.1.A, 6s6y.1.B, 6sdr.1.A, 6sdv.1.A, 6tg9.1.A, 6x89.1.H, 6yj4.1.G, 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, 7dbo.1.A, 7dbo.2.A, 7dg7.1.A, 7dg9.1.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, 7e5z.1.A, 7l5i.1.A, 7l5s.1.A, 7nz1.1.E, 7p61.1.C, 7p63.1.C, 7q5y.1.A, 7qsd.1.G, 7qv7.1.L, 7qv7.1.O, 7t2r.1.A, 7t30.1.A, 7tgh.58.A, 7ur8.1.A, 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, 7zm7.1.I, 8b9z.1.G, 8ba0.1.G, 8bqg.1.A, 8e73.55.A, 8e9g.1.G

Model Building Report

Results

Models

Model #01

Excluded ligands

Model #02

Excluded ligands

Model #03

Excluded ligands

Model #04

Excluded ligands

Materials and Methods

Template Search

Template Selection

Model Building

Model Quality Estimation

Ligand Modelling

Oligomeric State Conservation

References

Table T1:

Table T2: