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SWISS-MODEL Homology Modelling Report |
Model Building Report
This document lists the results for the homology modelling project "13_May_SF_Bin61_scaffold_51921_c1:3-1277_1" submitted to SWISS-MODEL workspace on March 29, 2023, 5:44 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 184 templates were found (Table T2).
Models
The following model was 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
|
0.74 | 0.70 ± 0.05 |
|
|
| Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description |
|---|---|---|---|---|---|---|---|---|---|---|
| 7b04.1.B | 42.51 | monomer | 0.00 | HHblits | X-ray | 2.97Å | 0.41 | 1 - 415 | 0.96 | 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 EVLARVGHKLAEQTGDARFADVWKLVDEKRTDAHLQRILDHSSNTKGYDALDLEAKAKKGIP----TLMMNRTYPKAVGY
7b04.1.B KILAGMASKLGELLRDKRFEDNWKFAIEGRASVYINRLLDGSTTMKGYTCEDIL---NGKYGEPGVAMLLFRTYPRHPFW
Target EQVADSRPWYTKSGRLEFYRDEDEFIEAGENLPVHREPIDSTFYEPNVIVSAPHEALRPAGPEDYGVELSDMSGEIRQGR
7b04.1.B EQVHESLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGPEATPYLPNAIVS-TNPYIR---PDDYGIPENAEYWEDRTVR
Target NVVKAWAELKKTPHPLAKDGYRFVFHTPKYRHGAHTMPIDTDMVAMLFGPFGDVYRHDRRTPYVAEGYVDIHPSDAREIG
7b04.1.B NIKKSWEETKKTKNFLWEKGYHFYCVTPKSRHTVHSQWAVTDWNFIWNNNFGDPYRMDKRMPGVGEHQIHIHPQAARDLG
Target VEDGDYVFIDSDPEDRPFRGWQKNKRDYEFSRLLCRARYYPGTPRGVTRMWFNMYGATPGSVEGQKSREDGLAKNPRTNY
7b04.1.B IEDGDYVYVDANPADRPYEGWKPNDSFYKVSRLMLRAKYNPAYPYNCTMMKHSAWISSDKTVQAHETRPDGRALSP-SGY
Target QAMFRSGSHQSATRGWLKPTWMTDSLVRKGLFGQSIGKGFLPDVHCPTGAPRESIVKITKAEPGGLGAEGLWRPAALGLR
7b04.1.B QSSFRYGSQQSITRDWSMPMHQLDSLFHKAKIGMKFIFGFEADNHCINTVPKETLVKITKAENGGMGGKGVWDPVKTGYT
Target PGYESKSMKTYLDGGYVDDADRQGGQG
7b04.1.B AGNENDFMKKFLNGELIKV--------
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.
FIEAGENLPVHREPIDSTFYEPNVIVSAPHEALRPAGPEDYGVELSDMSGEIRQGRNVVKAWAELKKTPHPLAKDGYRFVFHTPKYRHGAHTMPIDTDMV
AMLFGPFGDVYRHDRRTPYVAEGYVDIHPSDAREIGVEDGDYVFIDSDPEDRPFRGWQKNKRDYEFSRLLCRARYYPGTPRGVTRMWFNMYGATPGSVEG
QKSREDGLAKNPRTNYQAMFRSGSHQSATRGWLKPTWMTDSLVRKGLFGQSIGKGFLPDVHCPTGAPRESIVKITKAEPGGLGAEGLWRPAALGLRPGYE
SKSMKTYLDGGYVDDADRQGGQG
Table T2:
| Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description |
|---|---|---|---|---|---|---|---|---|---|
| 7b04.1.B | 42.51 | monomer | - | HHblits | X-ray | 2.97Å | 0.41 | 0.96 | Nitrite oxidoreductase subunit A |
| 7b04.1.B | 43.24 | monomer | - | BLAST | X-ray | 2.97Å | 0.41 | 0.96 | Nitrite oxidoreductase subunit A |
| 7b04.2.B | 42.51 | monomer | - | HHblits | X-ray | 2.97Å | 0.41 | 0.96 | Nitrite oxidoreductase subunit A |
| 7b04.2.B | 43.24 | monomer | - | BLAST | X-ray | 2.97Å | 0.41 | 0.96 | Nitrite oxidoreductase subunit A |
| 4ydd.1.A | 29.60 | monomer | - | HHblits | X-ray | 1.86Å | 0.35 | 0.53 | DMSO reductase family type II enzyme, molybdopterin subunit |
| 5e7o.1.A | 29.46 | monomer | - | HHblits | X-ray | 2.40Å | 0.35 | 0.53 | DMSO reductase family type II enzyme, molybdopterin subunit |
| 1q16.1.A | 27.01 | monomer | - | HHblits | X-ray | 1.90Å | 0.33 | 0.50 | Respiratory nitrate reductase 1 alpha chain |
| 1r27.4.A | 27.49 | monomer | - | HHblits | X-ray | 2.00Å | 0.33 | 0.50 | Respiratory nitrate reductase 1 alpha chain |
| 3ir5.1.A | 27.62 | monomer | - | HHblits | X-ray | 2.30Å | 0.33 | 0.50 | Respiratory nitrate reductase 1 alpha chain |
| 3egw.1.A | 27.54 | monomer | - | HHblits | X-ray | 1.90Å | 0.33 | 0.49 | Respiratory nitrate reductase 1 alpha chain |
| 3ir7.1.A | 26.67 | monomer | - | HHblits | X-ray | 2.50Å | 0.32 | 0.50 | Respiratory nitrate reductase 1 alpha chain |
| 3ir6.1.A | 27.05 | monomer | - | HHblits | X-ray | 2.80Å | 0.33 | 0.49 | Respiratory nitrate reductase 1 alpha chain |
| 7l5s.1.A | 24.71 | monomer | - | HHblits | X-ray | 2.09Å | 0.31 | 0.20 | Trimethylamine-N-oxide reductase |
| 7l5i.1.A | 24.71 | monomer | - | HHblits | X-ray | 1.73Å | 0.31 | 0.20 | Trimethylamine-N-oxide reductase |
| 1e60.1.A | 17.65 | monomer | - | HHblits | X-ray | 2.00Å | 0.29 | 0.20 | Dimethyl sulfoxide/trimethylamine N-oxide reductase |
| 1g8j.1.A | 22.89 | monomer | - | HHblits | X-ray | 2.03Å | 0.32 | 0.20 | ARSENITE OXIDASE |
| 1e18.1.A | 17.44 | monomer | - | HHblits | X-ray | 2.00Å | 0.29 | 0.20 | DMSO REDUCTASE. |
| 4aay.1.A | 24.10 | monomer | - | HHblits | X-ray | 2.70Å | 0.33 | 0.20 | AROA |
| 2iv2.1.A | 25.00 | monomer | - | HHblits | X-ray | 2.27Å | 0.33 | 0.20 | Formate dehydrogenase H |
| 1e5v.2.A | 17.44 | monomer | - | HHblits | X-ray | 2.40Å | 0.30 | 0.20 | Dimethyl sulfoxide/trimethylamine N-oxide reductase |
| 4dmr.1.A | 17.65 | monomer | - | HHblits | X-ray | 1.90Å | 0.29 | 0.20 | DMSO REDUCTASE |
| 1fdo.1.A | 25.00 | monomer | - | HHblits | X-ray | 2.80Å | 0.33 | 0.20 | FORMATE DEHYDROGENASE H |
| 1g8k.1.A | 22.89 | monomer | - | HHblits | X-ray | 1.64Å | 0.32 | 0.20 | ARSENITE OXIDASE |
| 1dms.1.A | 17.65 | monomer | - | HHblits | X-ray | 1.88Å | 0.29 | 0.20 | DMSO REDUCTASE |
| 1aa6.1.A | 25.00 | monomer | - | HHblits | X-ray | 2.30Å | 0.33 | 0.20 | FORMATE DEHYDROGENASE H |
| 7z0t.1.G | 25.00 | monomer | - | HHblits | EM | NA | 0.33 | 0.20 | Formate dehydrogenase H |
| 5nqd.1.A | 24.10 | monomer | - | HHblits | X-ray | 2.20Å | 0.33 | 0.20 | AroA |
| 4ydd.1.A | 37.65 | monomer | - | BLAST | X-ray | 1.86Å | 0.39 | 0.20 | DMSO reductase family type II enzyme, molybdopterin subunit |
| 5e7o.1.A | 37.65 | monomer | - | BLAST | X-ray | 2.40Å | 0.39 | 0.20 | DMSO reductase family type II enzyme, molybdopterin subunit |
| 6zjn.1.C | 19.23 | monomer | - | HHblits | EM | NA | 0.30 | 0.12 | NADH-quinone oxidoreductase subunit 3 |
| 3m9s.1.C | 19.23 | monomer | - | HHblits | X-ray | 4.50Å | 0.30 | 0.12 | NADH-quinone oxidoreductase subunit 3 |
| 6zjy.1.C | 19.23 | monomer | - | HHblits | EM | NA | 0.30 | 0.12 | NADH-quinone oxidoreductase subunit 3 |
| 6zjl.1.C | 19.23 | monomer | - | HHblits | EM | NA | 0.30 | 0.12 | NADH-quinone oxidoreductase subunit 3 |
| 6q8o.1.C | 19.23 | monomer | - | HHblits | X-ray | 3.61Å | 0.30 | 0.12 | NADH-quinone oxidoreductase subunit 3 |
| 3tiw.1.A | 17.02 | monomer | - | HHblits | X-ray | 1.80Å | 0.28 | 0.11 | Transitional endoplasmic reticulum ATPase |
| 3tiw.2.A | 17.02 | monomer | - | HHblits | X-ray | 1.80Å | 0.28 | 0.11 | Transitional endoplasmic reticulum ATPase |
| 6ziy.1.C | 19.23 | monomer | - | HHblits | EM | NA | 0.30 | 0.12 | NADH-quinone oxidoreductase subunit 3 |
| 7wbb.1.A | 19.30 | homo-tetramer | - | HHblits | EM | NA | 0.30 | 0.13 | AFG2 isoform 1 |
| 7wbb.1.C | 19.30 | homo-tetramer | - | HHblits | EM | NA | 0.30 | 0.13 | AFG2 isoform 1 |
| 7wbb.1.E | 19.30 | homo-tetramer | - | HHblits | EM | NA | 0.30 | 0.13 | AFG2 isoform 1 |
| 7wbb.1.D | 19.30 | homo-tetramer | - | HHblits | EM | NA | 0.30 | 0.13 | AFG2 isoform 1 |
| 7wbb.1.B | 19.30 | homo-tetramer | - | HHblits | EM | NA | 0.30 | 0.13 | AFG2 isoform 1 |
| 7wbb.1.G | 19.30 | homo-tetramer | - | HHblits | EM | NA | 0.30 | 0.13 | AFG2 isoform 1 |
| 4kdi.2.A | 16.00 | monomer | - | HHblits | X-ray | 1.86Å | 0.26 | 0.12 | Transitional endoplasmic reticulum ATPase |
| 4kdi.1.A | 16.00 | monomer | - | HHblits | X-ray | 1.86Å | 0.26 | 0.12 | Transitional endoplasmic reticulum ATPase |
| 3qwz.1.A | 16.33 | monomer | - | HHblits | X-ray | 2.00Å | 0.27 | 0.12 | Transitional endoplasmic reticulum ATPase |
| 3qc8.1.A | 16.67 | monomer | - | HHblits | X-ray | 2.20Å | 0.27 | 0.11 | Transitional endoplasmic reticulum ATPase |
| 4kdl.1.A | 16.00 | monomer | - | HHblits | X-ray | 1.81Å | 0.26 | 0.12 | Transitional endoplasmic reticulum ATPase |
| 2fug.2.C | 19.23 | monomer | - | HHblits | X-ray | 3.30Å | 0.30 | 0.12 | NADH-quinone oxidoreductase chain 3 |
| 5g4g.1.A | 21.28 | monomer | - | HHblits | EM | 7.80Å | 0.29 | 0.11 | VCP-LIKE ATPASE |
The table above shows the top 50 filtered templates. A further 117 templates were found which were considered to be less suitable for modelling than the filtered list.
1cz4.1.A, 1cz5.1.A, 1eu1.1.A, 1h0h.1.A, 1kqf.1.A, 1ogy.1.A, 1pqf.1.A, 1pqh.1.A, 1pt1.1.A, 1tmo.1.A, 1uhd.1.B, 1uhe.1.B, 1wlf.1.A, 1yle.1.A, 2c45.1.A, 2d9r.1.A, 2e7z.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, 3hu1.1.A, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3oug.1.A, 3pjy.1.A, 3pjy.1.B, 3plx.1.B, 3qq7.1.A, 3qq8.1.A, 4cs0.1.A, 4ga5.1.A, 4ga6.1.A, 4rv0.1.A, 4v4c.1.A, 5b6c.1.A, 5cuo.1.A, 5cup.1.A, 5e7p.1.A, 5epp.1.A, 5g4f.1.A, 5g4f.1.B, 5g4f.1.C, 5g4f.1.D, 5g4f.1.E, 5g4f.1.F, 5glf.1.A, 5glf.2.A, 5glf.3.A, 5glf.4.A, 5t5i.1.D, 5udf.1.A, 5x4l.1.A, 5x4l.2.A, 6cz7.1.A, 6f0k.1.B, 6f49.1.A, 6hd3.1.A, 6lod.1.B, 6sdr.1.A, 6sdv.1.A, 6tg9.1.A, 7bkb.1.J, 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, 7mdx.1.B, 7nz1.1.E, 7p61.1.C, 7p63.1.C, 7vw6.1.A, 8bqg.1.A, 8e9g.1.G