4_1_Jan_SF_Bin21_scaffold_19364_c1:2-1714_1

SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "4_1_Jan_SF_Bin21_scaffold_19364_c1:2-1714_1" submitted to SWISS-MODEL workspace on March 29, 2023, 5:45 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 266 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	0.71	0.69 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
7b04.1.B	39.29	monomer	0.00	HHblits	X-ray	2.97Å	0.39	28 - 567	0.93	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    FNGAPQYINENPFDLELDASRPARPRQYWRAESAHFYNHEDHP-----LRVGTRLLTGSTHMPTPTKVMWFANANSILGN
7b04.1.B  ---------------------------RALDEEVAYWNHSERPLIVNTPKYGRKVFTGKTHMPSPTKVLWFTNVNLINN-

Target    VKWHYNTVVNA-LPRMEMIAVHEWWWTGSCEWADVVFGVDSWGELKHPDMTASVTNPFLIVFPKTPIKRIFNTVGDIDVL
7b04.1.B  -AKHVYQMLKNVNPNIEQIMSTDIEITGSIEYADFAFPANSWVEFQEFEITNSCSNPFIQIWGKTGITPVYESKDDVKIL

Target    ALVSSKLAELTGDTRFNDMWKFVREGRTDVYLQRILDASTNTKGYRFTELEAKARE--GIPALMNSRTSPKVVGYDQLAD
7b04.1.B  AGMASKLGELLRDKRFEDNWKFAIEGRASVYINRLLDGSTTMKGYTCEDILNGKYGEPGVAM-LLFRTYPRHPFWEQVHE

Target    STPWYTKSGRLEFYREEDEFIEAGENLPVHREPVDSTFYEPNVIVSPKHEAVRPSGPEDYGVARTDLSCEVRCGRNVVLT
7b04.1.B  SLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGPEATPYLPNAIVSTN-PY---IRPDDYGIPENAEYWEDRTVRNIKKS

Target    WAETRQTQHPLVKQGHKFIFHTPKYRHGSHTTPIDTDMNAVLFGPFGDIYRRDKRSPFVTEGYVDINPTDGLELGLQDGD
7b04.1.B  WEETKKTKNFLWEKGYHFYCVTPKSRHTVHSQWAVTDWNFIWNNNFGDPYRMDKRMPGVGEHQIHIHPQAARDLGIEDGD

Target    YVWIDPDPEDRPFRGWQKNAKDMEFARLLCRARFYPGTPRGVTRMWFNMYGATPGSVRGAKARRDGLAKNPDTNYQAMFR
7b04.1.B  YVYVDANPADRPYEGWKPNDSFYKVSRLMLRAKYNPAYPYNCTMMKHSAWISSDKTVQAHETRPDGRALSP-SGYQSSFR

Target    SGSHQSATRGWLKPTWMTDSLVRKGLFGQGIGKGFLPDVHCPTGAPREAFVKISRAEPGGIGGQGLWRPAALGIRPRHES
7b04.1.B  YGSQQSITRDWSMPMHQLDSLFHKAKIGMKFIFGFEADNHCINTVPKETLVKITKAENGGMGGKGVWDPVKTGYTAGNEN

Target    PAMKRYLAGGFFSGPKE
7b04.1.B  DFMKKFLNGELIKVD--

Model #02	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.36	0.46 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
1q16.1.A	20.54	monomer	0.00	HHblits	X-ray	1.90Å	0.31	60 - 534	0.65	Respiratory nitrate reductase 1 alpha chain

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
3PH.12	Not in contact with model.	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
6MO.3	Binding site not conserved.	MOLYBDENUM(VI) ION
AGA.11	Binding site not conserved.	(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
F3S.10	Binding site not conserved.	FE3-S4 CLUSTER
HEM.4	Binding site not conserved.	PROTOPORPHYRIN IX CONTAINING FE
HEM.5	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
SF4.6	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
SF4.9	Binding site not conserved.	IRON/SULFUR CLUSTER

Target    FNGAPQYINENPFDLELDASRPARPRQYWRAESAHFYNHEDHPLRVGTRLLTGSTHMPTPTKVMWFANANSILGNVKWHY
1q16.1.A  -----------------------------------------------------------HPRNLFIWRSNLLGS--SGKG

Target    NT------------------------------V--VNALPRMEMIAVHEWWWTGSCEWADVVFGVDSWGELKHPDMTASV
1q16.1.A  HEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYEK--DDMNTSD

Target    TNPFLIVFPKTPIKRIFNTVGDIDVLALVSSKLAELTG----DT----RF----------------NDMWK---------
1q16.1.A  MHPFIHPLSA-AVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPIQHDSAAELAQPLDVKDWKKGECDLIPGK

Target    -----------------FVRE-G------------------RTDVYLQRI-------------------------LDAST
1q16.1.A  TAPHIMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAIDAAEMILTLAP

Target    NTKG----YRFTELEAKAR-----------EGIPALMN------------------SRTSPKVVGYDQLADSTPWYTKSG
1q16.1.A  ETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYTNVHELIPWRTLSG

Target    RLEFYREEDEFIEAGENLPVHREPVDSTFYEPNVIVSPKHEAVRPSGPEDYGVARTDLSCEVRCGRNVVLTWAETRQTQH
1q16.1.A  RQQLYQDHQWMRDFGESLLVYRPPIDTRSV-----------------KEVIGQ-------------------------KS

Target    PLVKQGHKFIFHTPKYRHGSHTTPIDTDMNAVLFGPFGDIYRRDKRSPFVTEGYVDINPTDGLELGLQDGDYVWIDPDPE
1q16.1.A  NG-NQEKALNFLTPHQKWGIHSTYSDNLLMLT----------LG-----RGGPVVWLSEADAKDLGIADNDWIEVFNSN-

Target    DRPFRGWQKNAKDMEFARLLCRARFYPGTPRGVTRMWFNMYGATPGSVRGAKARRDGLAKNPDTNYQAMFRSGSHQSATR
1q16.1.A  ----------------GALTARAVVSQRVPAGMTMMYHAQE---------RIVNLPGS-----EI--TQQRGGIHNSVTR

Target    GWLKPTWMTDSLVRKGLFGQGIGKGFLPDVHCPTGAPREAFVKISRAEPGGIGGQGLWRPAALGIRPRHESPAMKRYLAG
1q16.1.A  ITPKPTHMI------GGYA---HLAYGFNYYGTVGSNRDEFVVVRKMKNIDWL---------------------------

Target    GFFSGPKE
1q16.1.A  --------

Model #03	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.26	0.43 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
7p63.1.C	16.25	monomer	0.00	HHblits	EM	-	0.27	60 - 441	0.49	NADH-quinone oxidoreductase

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
3PE.15	Binding site not conserved.	1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.16	Binding site not conserved.	1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.18	Binding site not conserved.	1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.19	Binding site not conserved.	1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.20	Binding site not conserved.	1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.21	Binding site not conserved.	1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.24	Binding site not conserved.	1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.25	Binding site not conserved.	1,2-Distearoyl-sn-glycerophosphoethanolamine
CA.9	Binding site not conserved.	CALCIUM ION
DCQ.10	Binding site not conserved.	2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
FES.4	Binding site not conserved.	FE2/S2 (INORGANIC) CLUSTER
FES.8	Binding site not conserved.	FE2/S2 (INORGANIC) CLUSTER
FMN.2	Binding site not conserved.	FLAVIN MONONUCLEOTIDE
LFA.14	Binding site not conserved.	EICOSANE
LFA.17	Binding site not conserved.	EICOSANE
LFA.22	Binding site not conserved.	EICOSANE
LFA.23	Binding site not conserved.	EICOSANE
NAI.3	Binding site not conserved.	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
SF4.1	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.5	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
SF4.11	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.12	Binding site not conserved.	IRON/SULFUR CLUSTER
SF4.13	Binding site not conserved.	IRON/SULFUR CLUSTER

Target    FNGAPQYINENPFDLELDASRPARPRQYWRAESAHFYNHEDHPLRVGTRLLTGSTHMPTPTKVMWFANANSILGNVKWHY
7p63.1.C  -----------------------------------------------------------RADAVVVLE-NDLHR--HASA

Target    NTVVNALPRMEMIAVHEWWWTGSCEWADVVFGVDSWGELKHPDMTASVTNPFLIVFPKTPIKRIF-----NTVGDIDVLA
7p63.1.C  TRVNAALAKAPLVMVVDHQRTAIMENAHLVLSAASFAESD--GTVI-NNEGRAQRFFQ-VYDPAYYDSKTVMLESWRWLH

Target    LVSSKLAELTGDTRFNDMWKFVREGRTDVYLQRILDASTNTKGYRFTELEAKAR----------------------EGIP
7p63.1.C  SLHSTLLS----REV--DWTQL-----DHVIDAVVAKIPELAGIKDAAPDATFRIRGQKLAREPHRYSGRTAMRANISVH

Target    ALMN--------------------S---RTSPKVVGYDQL-ADSTPWYTKSGRLEFYREEDEFIEAG-ENLPVHREPVDS
7p63.1.C  EPRQPQDIDTMFTFSMEGNNQPTAHRSQVPFAWAPGWNSPQAWNKFQDEVGGKLRFGDPGVRLFETSENGLDYFTSVPAR

Target    TFYEPNVIVSPKHEAVRPSGPEDYGVARTDLSCEVRCGRNVVLTWAETRQTQHPLVKQGHKFIFHTPKYRHGSHTTPIDT
7p63.1.C  ------------------------------------------------------FQPQDGKWRIAPYYHLFGSDELSQRA

Target    DMNAVLFGPFGDIYRRDKRSPFVTEGYVDINPTDGLELGLQDGDYVWIDPDPEDRPFRGWQKNAKDMEFARLLCRARFYP
7p63.1.C  PVFQ-------------SRMP---QPYIKLNPADAAKLGVNAGTRVSFSYDG-----------------NTVTLPVEIAE

Target    GTPRGVTRMWFNMYGATPGSVRGAKARRDGLAKNPDTNYQAMFRSGSHQSATRGWLKPTWMTDSLVRKGLFGQGIGKGFL
7p63.1.C  GLTAGQVGLPMGM-------------------------------------------------------------------

Target    PDVHCPTGAPREAFVKISRAEPGGIGGQGLWRPAALGIRPRHESPAMKRYLAGGFFSGPKE
7p63.1.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.

FNGAPQYINENPFDLELDASRPARPRQYWRAESAHFYNHEDHPLRVGTRLLTGSTHMPTPTKVMWFANANSILGNVKWHYNTVVNALPRMEMIAVHEWWW
TGSCEWADVVFGVDSWGELKHPDMTASVTNPFLIVFPKTPIKRIFNTVGDIDVLALVSSKLAELTGDTRFNDMWKFVREGRTDVYLQRILDASTNTKGYR
FTELEAKAREGIPALMNSRTSPKVVGYDQLADSTPWYTKSGRLEFYREEDEFIEAGENLPVHREPVDSTFYEPNVIVSPKHEAVRPSGPEDYGVARTDLS
CEVRCGRNVVLTWAETRQTQHPLVKQGHKFIFHTPKYRHGSHTTPIDTDMNAVLFGPFGDIYRRDKRSPFVTEGYVDINPTDGLELGLQDGDYVWIDPDP
EDRPFRGWQKNAKDMEFARLLCRARFYPGTPRGVTRMWFNMYGATPGSVRGAKARRDGLAKNPDTNYQAMFRSGSHQSATRGWLKPTWMTDSLVRKGLFG
QGIGKGFLPDVHCPTGAPREAFVKISRAEPGGIGGQGLWRPAALGIRPRHESPAMKRYLAGGFFSGPKE

Table T2:

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Coverage	Description
7b04.1.B	39.29	monomer	-	HHblits	X-ray	2.97Å	0.39	0.93	Nitrite oxidoreductase subunit A
7b04.1.B	41.41	monomer	-	BLAST	X-ray	2.97Å	0.40	0.92	Nitrite oxidoreductase subunit A
7b04.2.B	39.29	monomer	-	HHblits	X-ray	2.97Å	0.39	0.93	Nitrite oxidoreductase subunit A
7b04.2.B	41.41	monomer	-	BLAST	X-ray	2.97Å	0.40	0.92	Nitrite oxidoreductase subunit A
4ydd.1.A	23.05	monomer	-	HHblits	X-ray	1.86Å	0.33	0.61	DMSO reductase family type II enzyme, molybdopterin subunit
5e7o.1.A	23.28	monomer	-	HHblits	X-ray	2.40Å	0.33	0.61	DMSO reductase family type II enzyme, molybdopterin subunit
2ivf.1.A	22.94	monomer	-	HHblits	X-ray	1.88Å	0.31	0.60	ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
1q16.1.A	20.54	monomer	-	HHblits	X-ray	1.90Å	0.31	0.65	Respiratory nitrate reductase 1 alpha chain
1r27.4.A	20.60	homo-dimer	0.00	HHblits	X-ray	2.00Å	0.31	0.65	Respiratory nitrate reductase 1 alpha chain
3ir5.1.A	20.49	monomer	-	HHblits	X-ray	2.30Å	0.31	0.65	Respiratory nitrate reductase 1 alpha chain
3egw.1.A	20.65	homo-dimer	0.06	HHblits	X-ray	1.90Å	0.31	0.65	Respiratory nitrate reductase 1 alpha chain
3ir6.1.A	20.44	monomer	-	HHblits	X-ray	2.80Å	0.31	0.64	Respiratory nitrate reductase 1 alpha chain
3ir7.1.A	20.81	monomer	-	HHblits	X-ray	2.50Å	0.31	0.65	Respiratory nitrate reductase 1 alpha chain
1e60.1.A	17.01	monomer	-	HHblits	X-ray	2.00Å	0.29	0.51	Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e5v.2.A	17.01	monomer	-	HHblits	X-ray	2.40Å	0.29	0.51	Dimethyl sulfoxide/trimethylamine N-oxide reductase
1dms.1.A	17.36	monomer	-	HHblits	X-ray	1.88Å	0.29	0.51	DMSO REDUCTASE
4dmr.1.A	17.01	monomer	-	HHblits	X-ray	1.90Å	0.30	0.51	DMSO REDUCTASE
1e18.1.A	17.77	monomer	-	HHblits	X-ray	2.00Å	0.30	0.50	DMSO REDUCTASE.
2iv2.1.A	15.97	monomer	-	HHblits	X-ray	2.27Å	0.29	0.46	Formate dehydrogenase H
1aa6.1.A	15.97	monomer	-	HHblits	X-ray	2.30Å	0.29	0.46	FORMATE DEHYDROGENASE H
7z0t.1.G	15.97	monomer	-	HHblits	EM	NA	0.29	0.46	Formate dehydrogenase H
7p63.1.C	16.25	monomer	-	HHblits	EM	NA	0.27	0.49	NADH-quinone oxidoreductase
1fdo.1.A	15.97	monomer	-	HHblits	X-ray	2.80Å	0.29	0.46	FORMATE DEHYDROGENASE H
7nz1.1.E	15.94	monomer	-	HHblits	EM	NA	0.27	0.49	NADH-quinone oxidoreductase subunit G
7p61.1.C	15.88	monomer	-	HHblits	EM	NA	0.27	0.49	NADH-quinone oxidoreductase
4ydd.1.A	26.37	monomer	-	BLAST	X-ray	1.86Å	0.34	0.35	DMSO reductase family type II enzyme, molybdopterin subunit
5e7o.1.A	26.37	monomer	-	BLAST	X-ray	2.40Å	0.34	0.35	DMSO reductase family type II enzyme, molybdopterin subunit
6sdr.1.A	14.85	monomer	-	HHblits	X-ray	2.10Å	0.26	0.18	Formate dehydrogenase, alpha subunit, selenocysteine-containing
8bqg.1.A	14.00	monomer	-	HHblits	X-ray	1.95Å	0.26	0.18	Formate dehydrogenase, alpha subunit, selenocysteine-containing
6sdv.1.A	14.00	monomer	-	HHblits	X-ray	1.90Å	0.26	0.18	Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit
7ak5.1.G	13.98	monomer	-	HHblits	EM	NA	0.25	0.16	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6gcs.1.A	17.39	monomer	-	HHblits	EM	4.32Å	0.28	0.16	75-KDA PROTEIN (NUAM)
7qsd.1.G	13.98	monomer	-	HHblits	EM	NA	0.26	0.16	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7aqr.1.F	12.09	monomer	-	HHblits	EM	NA	0.27	0.16	NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
6zk9.1.C	14.13	monomer	-	HHblits	EM	NA	0.26	0.16	NADH:ubiquinone oxidoreductase core subunit S1
7zd6.1.4	14.13	monomer	-	HHblits	EM	NA	0.26	0.16	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7v2c.1.L	15.22	monomer	-	HHblits	EM	NA	0.26	0.16	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7vxu.1.L	15.22	monomer	-	HHblits	EM	NA	0.26	0.16	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6yj4.1.G	17.39	monomer	-	HHblits	EM	NA	0.28	0.16	Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
6qc5.1.C	13.98	monomer	-	HHblits	EM	NA	0.26	0.16	NADH:ubiquinone oxidoreductase core subunit S1
6qcf.1.C	13.98	monomer	-	HHblits	EM	NA	0.26	0.16	NADH:ubiquinone oxidoreductase core subunit S1
7ar7.1.G	12.09	monomer	-	HHblits	EM	NA	0.27	0.16	NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
6rfq.1.A	17.39	monomer	-	HHblits	EM	3.30Å	0.28	0.16	Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
6rfs.1.A	17.39	monomer	-	HHblits	EM	4.04Å	0.28	0.16	Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
5o31.1.8	13.98	monomer	-	HHblits	EM	4.13Å	0.25	0.16	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
5gpn.24.A	15.05	monomer	-	HHblits	EM	NA	0.26	0.16	NADH-ubiquinone oxidoreductase 75 kDa subunit
7a23.1.O	12.09	monomer	-	HHblits	EM	NA	0.27	0.16	75kDa
7ar8.1.G	12.09	monomer	-	HHblits	EM	NA	0.27	0.16	NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
5xtb.1.L	15.22	monomer	-	HHblits	EM	NA	0.26	0.16	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7dgr.10.A	13.98	monomer	-	HHblits	EM	NA	0.25	0.16	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

The table above shows the top 50 filtered templates. A further 171 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, 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, 1kqf.1.A, 1ogy.1.A, 1q16.1.A, 1r27.4.A, 1tmo.1.A, 1wlf.1.A, 2e7z.1.A, 2fug.2.C, 2iv2.1.A, 2ivf.1.A, 2ki8.1.A, 2nya.1.A, 2pjh.1.B, 2v3v.1.A, 2v45.1.A, 2vpx.1.D, 2vpz.1.A, 3egw.1.A, 3hu1.1.A, 3ir5.1.A, 3ir6.1.A, 3ir7.1.A, 3m9s.1.C, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3qc8.1.A, 3qq7.1.A, 3qq8.1.A, 3qwz.1.A, 3tiw.1.A, 3tiw.2.A, 4aay.1.A, 4dmr.1.A, 4ga5.1.A, 4ga6.1.A, 4kdi.1.A, 4kdi.2.A, 4kdl.1.A, 4rv0.1.A, 4v4c.1.A, 4ydd.1.A, 5b6c.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, 5nqd.1.A, 5t5i.1.B, 5t5i.1.D, 5x4l.1.A, 5x4l.2.A, 6btm.1.B, 6cz7.1.A, 6f0k.1.B, 6g72.1.G, 6gcs.1.A, 6hd3.1.A, 6lod.1.B, 6q8o.1.C, 6rfq.1.A, 6rfs.1.A, 6s6y.1.B, 6sdr.1.A, 6sdv.1.A, 6tg9.1.A, 6x89.1.H, 6yj4.1.G, 6ziy.1.C, 6zjl.1.C, 6zjn.1.C, 6zjy.1.C, 6zr2.1.G, 7ak6.1.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, 7p61.1.C, 7p63.1.C, 7q5y.1.A, 7qv7.1.L, 7qv7.1.O, 7t2r.1.A, 7t30.1.A, 7tgh.58.A, 7vw6.1.A, 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

Materials and Methods

Template Search

Template Selection

Model Building

Model Quality Estimation

Ligand Modelling

Oligomeric State Conservation

References

Table T1:

Table T2: