4_1_Jan_SF_Bin61_scaffold_2525_c1:3-704_1

SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "4_1_Jan_SF_Bin61_scaffold_2525_c1:3-704_1" submitted to SWISS-MODEL workspace on March 29, 2023, 6:31 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 239 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	0.52	0.58 ± 0.06

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
7b04.1.B	46.45	monomer	0.00	BLAST	X-ray	2.97Å	0.45	48 - 233	0.79	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    MAQGVSRRQLLGRALALGSGAALADLLGPARFLSPAGAATAGAVVPGNPLRVMPDRTWEQIYRNQFEDDSTFVFTCAPND
7b04.1.B  -----------------------------------------------NPLDTYPDRRWESVYRDQYQYDRTFTYCCSPND

Target    THNCLLRAHVKNGVVVRISPTYGYGEATDLYGNRASHRWDPRTCQKGLILSRRFYSERRVKAPMIRKGFKDWVEAGYPRN
7b04.1.B  THACRIRAFVRNNVMMRVEQNYDHQNYSDLYGNKATRNWNPRMCLKGYTFHRRVYGPYRLRYPLIRKGWKRWADDGFP--

Target    DDGTPQMDVTL----RGSDDWIRISWDEATTIAAKTMEDVARTFNGDEGARKLLAQGYHPEMVEVMHGAGVQALKLR
7b04.1.B  -ELTPENKTKYMFDNRGNDELLRASWDEAFTYASKGIIHITKKYSGPEGAQKLIDQGYPKEMVDRMQGAGTRTFKGR

Model #02	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.2.1	monomer	None	0.47	0.46 ± 0.06

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
1q16.1.A	25.64	monomer	0.00	HHblits	X-ray	1.90Å	0.32	2 - 230	0.84	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    MAQGVSRRQLLGRALALGSGAALADLLGPARFLSPAGAATAGAVVPGNPLRVMPDRTWEQIYRNQFEDDSTFVFTCAPND
1q16.1.A  MSKFLDRFRYFKQKGETFADGH--------------------------GQLLNTNRDWEDGYRQRWQHDKIVRSTHGVNC

Target    THNCLLRAHVKNGVVVRISPTYGYGEATDLYGNRASHRWDPRTCQKGLILSRRFYSERRVKAPMIRKGF-KDWVEAGY--
1q16.1.A  TGSCSWKIYVKNGLVTWETQQTDYPR-----TRPDLPNHEPRGCPRGASYSWYLYSANRLKYPMMRKRLMKMWREAKALH

Target    --PR-------NDDGTPQMDVTLRGSDDWIRISWDEATTIAAKTMEDVARTFNGDEGARKLLAQGYHPEMVEVMHGAGVQ
1q16.1.A  SDPVEAWASIIEDADKAKSFKQARGRGGFVRSSWQEVNELIAASNVYTIKNYGPDR----VAGFSPIPAMSMVSYASGAR

Target    ALKLR
1q16.1.A  YL---

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.

MAQGVSRRQLLGRALALGSGAALADLLGPARFLSPAGAATAGAVVPGNPLRVMPDRTWEQIYRNQFEDDSTFVFTCAPNDTHNCLLRAHVKNGVVVRISP
TYGYGEATDLYGNRASHRWDPRTCQKGLILSRRFYSERRVKAPMIRKGFKDWVEAGYPRNDDGTPQMDVTLRGSDDWIRISWDEATTIAAKTMEDVARTF
NGDEGARKLLAQGYHPEMVEVMHGAGVQALKLR

Table T2:

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Coverage	Description
7b04.1.B	46.45	monomer	-	BLAST	X-ray	2.97Å	0.45	0.79	Nitrite oxidoreductase subunit A
7b04.2.B	46.45	monomer	-	BLAST	X-ray	2.97Å	0.45	0.79	Nitrite oxidoreductase subunit A
7b04.1.B	40.51	monomer	-	HHblits	X-ray	2.97Å	0.41	0.84	Nitrite oxidoreductase subunit A
7b04.2.B	40.51	monomer	-	HHblits	X-ray	2.97Å	0.41	0.84	Nitrite oxidoreductase subunit A
1q16.1.A	25.64	monomer	-	HHblits	X-ray	1.90Å	0.32	0.84	Respiratory nitrate reductase 1 alpha chain
3ir5.1.A	26.02	monomer	-	HHblits	X-ray	2.30Å	0.33	0.84	Respiratory nitrate reductase 1 alpha chain
3egw.1.A	27.68	homo-dimer	0.13	HHblits	X-ray	1.90Å	0.34	0.76	Respiratory nitrate reductase 1 alpha chain
3ir7.1.A	25.64	monomer	-	HHblits	X-ray	2.50Å	0.32	0.84	Respiratory nitrate reductase 1 alpha chain
1r27.4.A	25.39	homo-dimer	0.11	HHblits	X-ray	2.00Å	0.32	0.83	Respiratory nitrate reductase 1 alpha chain
3ir6.1.A	25.64	monomer	-	HHblits	X-ray	2.80Å	0.33	0.84	Respiratory nitrate reductase 1 alpha chain
3ir7.1.A	30.54	monomer	-	BLAST	X-ray	2.50Å	0.35	0.72	Respiratory nitrate reductase 1 alpha chain
3ir5.1.A	31.14	monomer	-	BLAST	X-ray	2.30Å	0.36	0.72	Respiratory nitrate reductase 1 alpha chain
1q16.1.A	30.54	monomer	-	BLAST	X-ray	1.90Å	0.35	0.72	Respiratory nitrate reductase 1 alpha chain
3egw.1.A	30.54	homo-dimer	0.13	BLAST	X-ray	1.90Å	0.35	0.72	Respiratory nitrate reductase 1 alpha chain
3ir6.1.A	30.54	monomer	-	BLAST	X-ray	2.80Å	0.35	0.72	Respiratory nitrate reductase 1 alpha chain
1r27.4.A	30.54	homo-dimer	0.13	BLAST	X-ray	2.00Å	0.35	0.72	Respiratory nitrate reductase 1 alpha chain
2ivf.1.A	31.47	monomer	-	BLAST	X-ray	1.88Å	0.37	0.61	ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
2ivf.1.A	26.95	monomer	-	HHblits	X-ray	1.88Å	0.32	0.72	ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
1kqf.1.A	28.17	homo-trimer	0.11	HHblits	X-ray	1.60Å	0.32	0.61	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT
4dmr.1.A	24.11	monomer	-	HHblits	X-ray	1.90Å	0.32	0.61	DMSO REDUCTASE
1e18.1.A	23.02	monomer	-	HHblits	X-ray	2.00Å	0.31	0.60	DMSO REDUCTASE.
1e60.1.A	24.11	monomer	-	HHblits	X-ray	2.00Å	0.32	0.61	Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e5v.2.A	22.14	monomer	-	HHblits	X-ray	2.40Å	0.31	0.60	Dimethyl sulfoxide/trimethylamine N-oxide reductase
8bqg.1.A	19.81	monomer	-	HHblits	X-ray	1.95Å	0.29	0.45	Formate dehydrogenase, alpha subunit, selenocysteine-containing
7l5s.1.A	31.37	monomer	-	HHblits	X-ray	2.09Å	0.36	0.44	Trimethylamine-N-oxide reductase
6sdv.1.A	20.57	monomer	-	HHblits	X-ray	1.90Å	0.29	0.61	Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit
6sdr.1.A	20.57	monomer	-	HHblits	X-ray	2.10Å	0.29	0.61	Formate dehydrogenase, alpha subunit, selenocysteine-containing
7l5i.1.A	31.37	monomer	-	HHblits	X-ray	1.73Å	0.36	0.44	Trimethylamine-N-oxide reductase
2iv2.1.A	27.37	monomer	-	HHblits	X-ray	2.27Å	0.33	0.41	Formate dehydrogenase H
1fdo.1.A	27.37	monomer	-	HHblits	X-ray	2.80Å	0.33	0.41	FORMATE DEHYDROGENASE H
7z0t.1.G	27.37	monomer	-	HHblits	EM	NA	0.33	0.41	Formate dehydrogenase H
1aa6.1.A	27.37	monomer	-	HHblits	X-ray	2.30Å	0.33	0.41	FORMATE DEHYDROGENASE H
6rfs.1.A	21.11	monomer	-	HHblits	EM	4.04Å	0.31	0.39	Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
6yj4.1.G	21.11	monomer	-	HHblits	EM	NA	0.31	0.39	Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
7ar7.1.G	18.89	monomer	-	HHblits	EM	NA	0.29	0.39	NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
6gcs.1.A	21.11	monomer	-	HHblits	EM	4.32Å	0.31	0.39	75-KDA PROTEIN (NUAM)
6rfq.1.A	21.11	monomer	-	HHblits	EM	3.30Å	0.31	0.39	Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
6zr2.1.G	16.48	monomer	-	HHblits	EM	3.10Å	0.28	0.39	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
2fug.2.C	17.78	monomer	-	HHblits	X-ray	3.30Å	0.31	0.39	NADH-quinone oxidoreductase chain 3
6g72.1.G	16.48	monomer	-	HHblits	EM	NA	0.28	0.39	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7ak6.1.G	16.48	monomer	-	HHblits	EM	NA	0.28	0.39	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
3m9s.1.C	17.78	monomer	-	HHblits	X-ray	4.50Å	0.31	0.39	NADH-quinone oxidoreductase subunit 3
6q8o.1.C	17.78	monomer	-	HHblits	X-ray	3.61Å	0.31	0.39	NADH-quinone oxidoreductase subunit 3
7nz1.1.E	18.95	monomer	-	HHblits	EM	NA	0.29	0.41	NADH-quinone oxidoreductase subunit G
7p63.1.C	18.95	monomer	-	HHblits	EM	NA	0.29	0.41	NADH-quinone oxidoreductase
6zjn.1.C	17.78	monomer	-	HHblits	EM	NA	0.31	0.39	NADH-quinone oxidoreductase subunit 3
7p61.1.C	19.15	monomer	-	HHblits	EM	NA	0.29	0.40	NADH-quinone oxidoreductase
6zjl.1.C	17.78	monomer	-	HHblits	EM	NA	0.31	0.39	NADH-quinone oxidoreductase subunit 3
6ziy.1.C	17.78	monomer	-	HHblits	EM	NA	0.31	0.39	NADH-quinone oxidoreductase subunit 3
6zjy.1.C	17.78	monomer	-	HHblits	EM	NA	0.31	0.39	NADH-quinone oxidoreductase subunit 3

The table above shows the top 50 filtered templates. A further 189 templates were found which were considered to be less suitable for modelling than the filtered list.
1bcc.1.O, 1be3.1.E, 1bgy.1.P, 1dms.1.A, 1eu1.1.A, 1fxk.1.C, 1g8j.1.A, 1g8k.1.A, 1h0h.1.A, 1kb9.1.E, 1l0l.1.E, 1l0n.1.E, 1ntk.1.E, 1ntm.1.E, 1ogy.1.A, 1q90.1.E, 1sqb.1.E, 1sqp.1.P, 1sqq.1.P, 1sqv.1.E, 1tmo.1.A, 1vf5.1.D, 1vf5.1.L, 1zrt.1.C, 1zrt.1.F, 2d2c.1.D, 2d2c.1.L, 2e75.1.D, 2e76.1.D, 2e7z.1.A, 2fyn.1.C, 2fyn.2.C, 2fyu.1.E, 2nya.1.A, 2o01.1.H, 2pq4.1.B, 2qjk.1.C, 2qjp.1.C, 2qjy.3.F, 2v3v.1.A, 2v45.1.A, 2vpx.1.D, 2vpz.1.A, 2ybb.1.b, 2zdi.1.C, 3bcc.1.E, 3cwb.1.E, 3h1h.1.E, 3h1h.1.O, 3h1i.1.E, 3l75.1.E, 3l75.1.O, 3lw5.1.H, 3o5a.1.A, 4aay.1.A, 4d6t.1.E, 4h44.1.D, 4ogq.1.L, 4pv1.1.L, 4u3f.1.E, 4v4c.1.A, 4ydd.1.A, 5e7o.1.A, 5gpn.17.A, 5gpn.24.A, 5gpn.5.A, 5gup.54.A, 5gup.56.A, 5j8k.55.A, 5kkz.1.C, 5kli.1.C, 5klv.1.P, 5nmi.1.E, 5nqd.1.A, 5o31.1.8, 5okd.1.E, 5t5i.1.B, 5xtb.1.L, 5xte.1.C, 6adq.1.L, 6btm.1.B, 6cz7.1.A, 6f0k.1.B, 6fo0.1.E, 6fo6.1.J, 6giq.1.E, 6hu9.1.E, 6hwh.1.A, 6lod.1.B, 6nhg.1.E, 6nin.1.C, 6nr8.1.C, 6nr8.1.E, 6nr9.1.S, 6nr9.1.U, 6nrb.1.S, 6nrb.1.U, 6nrc.1.C, 6nrc.1.E, 6nrd.1.S, 6nrd.1.U, 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, 6rqf.1.D, 6rqf.1.L, 6s6y.1.B, 6t0b.1.E, 6t0b.1.O, 6t15.1.E, 6t15.1.O, 6tg9.1.A, 6vy1.1.A, 6vy1.1.G, 6vy1.1.M, 6x89.1.H, 6ymx.1.Q, 6ymx.1.Z, 6zk9.1.C, 7a23.1.O, 7ak5.1.G, 7aqr.1.F, 7ar8.1.G, 7arc.1.F, 7bkb.1.F, 7bkb.1.L, 7dgr.10.A, 7dgr.60.A, 7dgs.50.A, 7dgs.60.A, 7e1v.1.P, 7e5z.1.A, 7jrg.1.E, 7l5i.1.A, 7l5s.1.A, 7o37.1.E, 7o37.1.O, 7o3c.1.E, 7o3c.1.O, 7o3h.1.E, 7o3h.1.O, 7q21.1.G, 7q5y.1.A, 7qhm.1.A, 7qhm.1.N, 7qho.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, 7wu7.1.E, 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, 8e73.55.A, 8e9g.1.G

Model Building Report

Results

Models

Model #01

Excluded ligands

Model #02

Excluded ligands

Materials and Methods

Template Search

Template Selection

Model Building

Model Quality Estimation

Ligand Modelling

Oligomeric State Conservation

References

Table T1:

Table T2: