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SWISS-MODEL Homology Modelling Report |
Model Building Report
This document lists the results for the homology modelling project "SP_0185" submitted to SWISS-MODEL workspace on May 24, 2021, 4:25 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 2021-05-19, PDB release 2021-05-14) was searched with BLAST (Camacho et al.) and HHblits (Steinegger et al.) for evolutionary related structures matching the target sequence in Table T1. For details on the template search, see Materials and Methods. Overall 296 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 | QMEAN |
|---|---|---|---|---|---|---|
|
PDB | ProMod3 3.2.0 | homo-pentamer (matching prediction) |
1 x MG: MAGNESIUM ION;
|
0.65 | -2.27 |
|
|
| Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description |
|---|---|---|---|---|---|---|---|---|---|---|
| 4ev6.1.A | 26.55 | homo-pentamer | 0.54 | HHblits | X-ray | 3.20Å | 0.34 | 17 - 314 | 0.92 | Magnesium transport protein CorA |
Included Ligands
| Ligand | Description |
|---|---|
| 1 x MG | MAGNESIUM ION |
Excluded ligands
| Ligand Name.Number | Reason for Exclusion | Description |
|---|---|---|
| MG.3 | Not in contact with model. | MAGNESIUM ION |
| MG.4 | Not in contact with model. | MAGNESIUM ION |
| MG.5 | Binding site not conserved. | MAGNESIUM ION |
| MG.6 | Not in contact with model. | MAGNESIUM ION |
| MG.7 | Not in contact with model. | MAGNESIUM ION |
| MG.8 | Not in contact with model. | MAGNESIUM ION |
| MG.9 | Binding site not conserved. | MAGNESIUM ION |
| MG.12 | Not in contact with model. | MAGNESIUM ION |
| MG.13 | Not in contact with model. | MAGNESIUM ION |
| MG.14 | Not in contact with model. | MAGNESIUM ION |
| MG.16 | Not in contact with model. | MAGNESIUM ION |
| MG.17 | Binding site not conserved. | MAGNESIUM ION |
| MG.18 | Not in contact with model. | MAGNESIUM ION |
| MG.20 | Binding site not conserved. | MAGNESIUM ION |
| MG.21 | Binding site not conserved. | MAGNESIUM ION |
| MG.22 | Not in contact with model. | MAGNESIUM ION |
| MG.23 | Binding site not conserved. | MAGNESIUM ION |
| MG.24 | Not in contact with model. | MAGNESIUM ION |
| MG.25 | Binding site not conserved. | MAGNESIUM ION |
| MG.26 | Not in contact with model. | MAGNESIUM ION |
| MG.27 | Binding site not conserved. | MAGNESIUM ION |
| MG.28 | Binding site not conserved. | MAGNESIUM ION |
| MG.29 | Binding site not conserved. | MAGNESIUM ION |
| MG.32 | Not in contact with model. | MAGNESIUM ION |
| MG.33 | Binding site not conserved. | MAGNESIUM ION |
| MG.34 | Binding site not conserved. | MAGNESIUM ION |
| MG.35 | Binding site not conserved. | MAGNESIUM ION |
| MG.36 | Binding site not conserved. | MAGNESIUM ION |
| MG.37 | Not in contact with model. | MAGNESIUM ION |
| MG.39 | Binding site not conserved. | MAGNESIUM ION |
| MG.40 | Binding site not conserved. | MAGNESIUM ION |
| UMQ.1 | Binding site not conserved. | UNDECYL-MALTOSIDE |
| UMQ.2 | Binding site not conserved. | UNDECYL-MALTOSIDE |
| UMQ.10 | Binding site not conserved. | UNDECYL-MALTOSIDE |
| UMQ.11 | Binding site not conserved. | UNDECYL-MALTOSIDE |
| UMQ.15 | Binding site not conserved. | UNDECYL-MALTOSIDE |
| UMQ.19 | Binding site not conserved. | UNDECYL-MALTOSIDE |
| UMQ.30 | Binding site not conserved. | UNDECYL-MALTOSIDE |
| UMQ.31 | Binding site not conserved. | UNDECYL-MALTOSIDE |
Target MKQVFLSTTTEFKEIDTLEPGTWINLVNPTQNESLEIANTFDIDIADLRAPLDAEEMSRITIEDEYTLIIVDVPVTEERN
4ev6.1.A ----------------EDYRLIWIDCYDPKDEELYKLSKKIGISVSDLQIGLDEQEIPRVEEDEDFYLIIYKAPLFEE--
Target NRTYYVTIPLGIIITEETIITTCLEPLPVLDVFINRRLRNFYT----FMRSRFIFQILYRNAELYLTALRSIDRKSEQIE
4ev6.1.A ---DITTTSLGIYIKNNLLLTIHSDKIKAIGRLHKLISTKKPRIVFERGIGFLLYHILNEITRSYSRILMNLEDELEELE
Target SQLHQSTRNEELIELMELEKTIVYFKASLKTNERVIKKLTSSTSNIKKYLEDEDLLEDTLIETQQAIEMADIYGNVLHSM
4ev6.1.A DKLLAGYDREVMEKILGLRKTLVYFHKSLIANRDVLVLLKRKYLPI-TTKEDRENFEDLYYDTLQLIDMSATYREVLTSM
Target TETFASIISNNQNNIMKTLALVTIVMSIPTMVFSAYGMNFKDNEIPLNGEPNAFWLIVFIAFAMSVSLTLYLIHKKWF
4ev6.1.A MDITLSLENIKMNQIMKILTMVTTIFAVPMWITGIYGMNFSY--LPLANNPQGFWLVMALMVVIIMIFVYIFRRSGWI
Target MKQVFLSTTTEFKEIDTLEPGTWINLVNPTQNESLEIANTFDIDIADLRAPLDAEEMSRITIEDEYTLIIVDVPVTEERN
4ev6.1.B ----------------EDYRLIWIDCYDPKDEELYKLSKKIGISVSDLQIGLDEQEIPRVEEDEDFYLIIYKAPLFEE--
Target NRTYYVTIPLGIIITEETIITTCLEPLPVLDVFINRRLRNFYT----FMRSRFIFQILYRNAELYLTALRSIDRKSEQIE
4ev6.1.B ---DITTTSLGIYIKNNLLLTIHSDKIKAIGRLHKLISTKKPRIVFERGIGFLLYHILNEITRSYSRILMNLEDELEELE
Target SQLHQSTRNEELIELMELEKTIVYFKASLKTNERVIKKLTSSTSNIKKYLEDEDLLEDTLIETQQAIEMADIYGNVLHSM
4ev6.1.B DKLLAGYDREVMEKILGLRKTLVYFHKSLIANRDVLVLLKRKYLPI-TTKEDRENFEDLYYDTLQLIDMSATYREVLTSM
Target TETFASIISNNQNNIMKTLALVTIVMSIPTMVFSAYGMNFKDNEIPLNGEPNAFWLIVFIAFAMSVSLTLYLIHKKWF
4ev6.1.B MDITLSLENIKMNQIMKILTMVTTIFAVPMWITGIYGMNFSY--LPLANNPQGFWLVMALMVVIIMIFVYIFRRSGWI
Target MKQVFLSTTTEFKEIDTLEPGTWINLVNPTQNESLEIANTFDIDIADLRAPLDAEEMSRITIEDEYTLIIVDVPVTEERN
4ev6.1.C ----------------EDYRLIWIDCYDPKDEELYKLSKKIGISVSDLQIGLDEQEIPRVEEDEDFYLIIYKAPLFEE--
Target NRTYYVTIPLGIIITEETIITTCLEPLPVLDVFINRRLRNFYT----FMRSRFIFQILYRNAELYLTALRSIDRKSEQIE
4ev6.1.C ---DITTTSLGIYIKNNLLLTIHSDKIKAIGRLHKLISTKKPRIVFERGIGFLLYHILNEITRSYSRILMNLEDELEELE
Target SQLHQSTRNEELIELMELEKTIVYFKASLKTNERVIKKLTSSTSNIKKYLEDEDLLEDTLIETQQAIEMADIYGNVLHSM
4ev6.1.C DKLLAGYDREVMEKILGLRKTLVYFHKSLIANRDVLVLLKRKYLPI-TTKEDRENFEDLYYDTLQLIDMSATYREVLTSM
Target TETFASIISNNQNNIMKTLALVTIVMSIPTMVFSAYGMNFKDNEIPLNGEPNAFWLIVFIAFAMSVSLTLYLIHKKWF
4ev6.1.C MDITLSLENIKMNQIMKILTMVTTIFAVPMWITGIYGMNFSY--LPLANNPQGFWLVMALMVVIIMIFVYIFRRSGWI
Target MKQVFLSTTTEFKEIDTLEPGTWINLVNPTQNESLEIANTFDIDIADLRAPLDAEEMSRITIEDEYTLIIVDVPVTEERN
4ev6.1.D ----------------EDYRLIWIDCYDPKDEELYKLSKKIGISVSDLQIGLDEQEIPRVEEDEDFYLIIYKAPLFEE--
Target NRTYYVTIPLGIIITEETIITTCLEPLPVLDVFINRRLRNFYT----FMRSRFIFQILYRNAELYLTALRSIDRKSEQIE
4ev6.1.D ---DITTTSLGIYIKNNLLLTIHSDKIKAIGRLHKLISTKKPRIVFERGIGFLLYHILNEITRSYSRILMNLEDELEELE
Target SQLHQSTRNEELIELMELEKTIVYFKASLKTNERVIKKLTSSTSNIKKYLEDEDLLEDTLIETQQAIEMADIYGNVLHSM
4ev6.1.D DKLLAGYDREVMEKILGLRKTLVYFHKSLIANRDVLVLLKRKYLPI-TTKEDRENFEDLYYDTLQLIDMSATYREVLTSM
Target TETFASIISNNQNNIMKTLALVTIVMSIPTMVFSAYGMNFKDNEIPLNGEPNAFWLIVFIAFAMSVSLTLYLIHKKWF
4ev6.1.D MDITLSLENIKMNQIMKILTMVTTIFAVPMWITGIYGMNFSY--LPLANNPQGFWLVMALMVVIIMIFVYIFRRSGWI
Target MKQVFLSTTTEFKEIDTLEPGTWINLVNPTQNESLEIANTFDIDIADLRAPLDAEEMSRITIEDEYTLIIVDVPVTEERN
4ev6.1.E ----------------EDYRLIWIDCYDPKDEELYKLSKKIGISVSDLQIGLDEQEIPRVEEDEDFYLIIYKAPLFEE--
Target NRTYYVTIPLGIIITEETIITTCLEPLPVLDVFINRRLRNFYT----FMRSRFIFQILYRNAELYLTALRSIDRKSEQIE
4ev6.1.E ---DITTTSLGIYIKNNLLLTIHSDKIKAIGRLHKLISTKKPRIVFERGIGFLLYHILNEITRSYSRILMNLEDELEELE
Target SQLHQSTRNEELIELMELEKTIVYFKASLKTNERVIKKLTSSTSNIKKYLEDEDLLEDTLIETQQAIEMADIYGNVLHSM
4ev6.1.E DKLLAGYDREVMEKILGLRKTLVYFHKSLIANRDVLVLLKRKYLPI-TTKEDRENFEDLYYDTLQLIDMSATYREVLTSM
Target TETFASIISNNQNNIMKTLALVTIVMSIPTMVFSAYGMNFKDNEIPLNGEPNAFWLIVFIAFAMSVSLTLYLIHKKWF
4ev6.1.E MDITLSLENIKMNQIMKILTMVTTIFAVPMWITGIYGMNFSY--LPLANNPQGFWLVMALMVVIIMIFVYIFRRSGWI
Model #02 |
File | Built with | Oligo-State | Ligands | GMQE | QMEAN |
|---|---|---|---|---|---|---|
|
PDB | ProMod3 3.2.0 | homo-trimer (matching prediction) |
None
|
0.07 | -3.73 |
|
|
| Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description |
|---|---|---|---|---|---|---|---|---|---|---|
| 6b7n.1.A | 14.29 | homo-trimer | 0.00 | HHblits | EM | - | 0.28 | 137 - 227 | 0.27 | Spike protein |
Excluded ligands
| Ligand Name.Number | Reason for Exclusion | Description |
|---|---|---|
| NAG.16 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.17 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.18 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.19 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.20 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.21 | Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.22 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.23 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.24 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.25 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.26 | Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.27 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.28 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.29 | Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.30 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.31 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.32 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.33 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.34 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.35 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.36 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.37 | Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.38 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG.39 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.1 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.2 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.3 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.5 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.6 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.7 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.8 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.10 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.11 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.12 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.13 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG.15 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG-NAG.4 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG-NAG.9 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
| NAG-NAG-NAG.14 | Binding site not conserved. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
Target MKQVFLSTTTEFKEIDTLEPGTWINLVNPTQNESLEIANTFDIDIADLRAPLDAEEMSRITIEDEYTLIIVDVPVTEERN
6b7n.1.A --------------------------------------------------------------------------------
Target NRTYYVTIPLGIIITEETIITTCLEPLPVLDVFINRRLRNFYTFMRSRFIFQILYRNAELYLTALRSIDRKSEQIESQLH
6b7n.1.A --------------------------------------------------------LAESFNQAVGNISLALSSVNDAIQ
Target QSTRNEELIELMELEKTIVYFKASLKTNERVIKKLTSSTSNIKKYLEDEDLLEDTLIETQQAIEMADIYGNVLHSMTETF
6b7n.1.A QTS-----EALNTVAIAIKKIQTVVNQQGEALSHLTAQLSN--NFQAISTSIQDIYNRLEEVEANQQ-------------
Target ASIISNNQNNIMKTLALVTIVMSIPTMVFSAYGMNFKDNEIPLNGEPNAFWLIVFIAFAMSVSLTLYLIHKKWF
6b7n.1.A --------------------------------------------------------------------------
Target MKQVFLSTTTEFKEIDTLEPGTWINLVNPTQNESLEIANTFDIDIADLRAPLDAEEMSRITIEDEYTLIIVDVPVTEERN
6b7n.1.B --------------------------------------------------------------------------------
Target NRTYYVTIPLGIIITEETIITTCLEPLPVLDVFINRRLRNFYTFMRSRFIFQILYRNAELYLTALRSIDRKSEQIESQLH
6b7n.1.B --------------------------------------------------------LAESFNQAVGNISLALSSVNDAIQ
Target QSTRNEELIELMELEKTIVYFKASLKTNERVIKKLTSSTSNIKKYLEDEDLLEDTLIETQQAIEMADIYGNVLHSMTETF
6b7n.1.B QTS-----EALNTVAIAIKKIQTVVNQQGEALSHLTAQLSN--NFQAISTSIQDIYNRLEEVEANQQ-------------
Target ASIISNNQNNIMKTLALVTIVMSIPTMVFSAYGMNFKDNEIPLNGEPNAFWLIVFIAFAMSVSLTLYLIHKKWF
6b7n.1.B --------------------------------------------------------------------------
Target MKQVFLSTTTEFKEIDTLEPGTWINLVNPTQNESLEIANTFDIDIADLRAPLDAEEMSRITIEDEYTLIIVDVPVTEERN
6b7n.1.C --------------------------------------------------------------------------------
Target NRTYYVTIPLGIIITEETIITTCLEPLPVLDVFINRRLRNFYTFMRSRFIFQILYRNAELYLTALRSIDRKSEQIESQLH
6b7n.1.C --------------------------------------------------------LAESFNQAVGNISLALSSVNDAIQ
Target QSTRNEELIELMELEKTIVYFKASLKTNERVIKKLTSSTSNIKKYLEDEDLLEDTLIETQQAIEMADIYGNVLHSMTETF
6b7n.1.C QTS-----EALNTVAIAIKKIQTVVNQQGEALSHLTAQLSN--NFQAISTSIQDIYNRLEEVEANQQ-------------
Target ASIISNNQNNIMKTLALVTIVMSIPTMVFSAYGMNFKDNEIPLNGEPNAFWLIVFIAFAMSVSLTLYLIHKKWF
6b7n.1.C --------------------------------------------------------------------------
Materials and Methods
Template Search
Template search with BLAST and HHblits has been performed against the SWISS-MODEL template library (SMTL, last update: 2021-05-19, last included PDB release: 2021-05-14).
The target sequence was searched with BLAST against the primary amino acid sequence contained in the SMTL. A total of 5 templates were found.
An initial HHblits profile has been built using the procedure outlined in (Steinegger et al.), followed by 1 iteration of HHblits against Uniclust30 (Mirdita, von den Driesch et al.). The obtained profile has then be searched against all profiles of the SMTL. A total of 335 templates were found.
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).
- Uniclust30
Mirdita, M., von den Driesch, L., Galiez, C., Martin, M.J., Söding, J., Steinegger, M. Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Research 45, D170–D176 (2016).
Table T1:
Primary amino acid sequence for which templates were searched and models were built.
MKQVFLSTTTEFKEIDTLEPGTWINLVNPTQNESLEIANTFDIDIADLRAPLDAEEMSRITIEDEYTLIIVDVPVTEERNNRTYYVTIPLGIIITEETII
TTCLEPLPVLDVFINRRLRNFYTFMRSRFIFQILYRNAELYLTALRSIDRKSEQIESQLHQSTRNEELIELMELEKTIVYFKASLKTNERVIKKLTSSTS
NIKKYLEDEDLLEDTLIETQQAIEMADIYGNVLHSMTETFASIISNNQNNIMKTLALVTIVMSIPTMVFSAYGMNFKDNEIPLNGEPNAFWLIVFIAFAM
SVSLTLYLIHKKWF
TTCLEPLPVLDVFINRRLRNFYTFMRSRFIFQILYRNAELYLTALRSIDRKSEQIESQLHQSTRNEELIELMELEKTIVYFKASLKTNERVIKKLTSSTS
NIKKYLEDEDLLEDTLIETQQAIEMADIYGNVLHSMTETFASIISNNQNNIMKTLALVTIVMSIPTMVFSAYGMNFKDNEIPLNGEPNAFWLIVFIAFAM
SVSLTLYLIHKKWF
Table T2:
| Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description |
|---|---|---|---|---|---|---|---|---|---|
| 4ev6.1.E | 26.55 | homo-pentamer | 0.54 | HHblits | X-ray | 3.20Å | 0.34 | 0.92 | Magnesium transport protein CorA |
| 4ev6.1.C | 26.55 | homo-pentamer | 0.54 | HHblits | X-ray | 3.20Å | 0.34 | 0.92 | Magnesium transport protein CorA |
| 4ev6.1.A | 26.55 | homo-pentamer | 0.54 | HHblits | X-ray | 3.20Å | 0.34 | 0.92 | Magnesium transport protein CorA |
| 4ev6.1.D | 26.55 | homo-pentamer | 0.54 | HHblits | X-ray | 3.20Å | 0.34 | 0.92 | Magnesium transport protein CorA |
| 4ev6.1.B | 26.55 | homo-pentamer | 0.54 | HHblits | X-ray | 3.20Å | 0.34 | 0.92 | Magnesium transport protein CorA |
| 4eed.1.C | 16.84 | homo-pentamer | 0.54 | HHblits | X-ray | 3.92Å | 0.30 | 0.95 | Magnesium transport protein CorA |
| 3jcf.1.E | 16.78 | homo-pentamer | 0.50 | HHblits | EM | NA | 0.30 | 0.93 | Magnesium transport protein CorA |
| 4eeb.1.A | 16.84 | homo-pentamer | 0.42 | HHblits | X-ray | 3.80Å | 0.30 | 0.95 | Magnesium transport protein CorA |
| 4eeb.1.B | 16.84 | homo-pentamer | 0.42 | HHblits | X-ray | 3.80Å | 0.30 | 0.95 | Magnesium transport protein CorA |
| 2hn2.1.C | 16.78 | homo-pentamer | 0.48 | HHblits | X-ray | 3.70Å | 0.30 | 0.93 | Magnesium transport protein corA |
| 2bbj.1.A | 16.78 | homo-pentamer | 0.44 | HHblits | X-ray | 3.90Å | 0.30 | 0.93 | divalent cation transport-related protein |
| 4ev6.1.C | 31.47 | homo-pentamer | 0.41 | BLAST | X-ray | 3.20Å | 0.36 | 0.80 | Magnesium transport protein CorA |
| 4ev6.1.E | 31.47 | homo-pentamer | 0.41 | BLAST | X-ray | 3.20Å | 0.36 | 0.80 | Magnesium transport protein CorA |
| 4ev6.1.A | 31.47 | homo-pentamer | 0.41 | BLAST | X-ray | 3.20Å | 0.36 | 0.80 | Magnesium transport protein CorA |
| 4ev6.1.D | 31.47 | homo-pentamer | 0.41 | BLAST | X-ray | 3.20Å | 0.36 | 0.80 | Magnesium transport protein CorA |
| 4ev6.1.B | 31.47 | homo-pentamer | 0.41 | BLAST | X-ray | 3.20Å | 0.36 | 0.80 | Magnesium transport protein CorA |
| 2iub.1.C | 16.78 | homo-pentamer | 0.32 | HHblits | X-ray | 2.90Å | 0.30 | 0.93 | DIVALENT CATION TRANSPORT-RELATED PROTEIN |
| 2iub.1.A | 16.78 | homo-pentamer | 0.32 | HHblits | X-ray | 2.90Å | 0.30 | 0.93 | DIVALENT CATION TRANSPORT-RELATED PROTEIN |
| 5n9y.1.B | 14.43 | homo-pentamer | 0.30 | HHblits | EM | NA | 0.27 | 0.93 | Zinc transport protein ZntB |
| 5n9y.1.C | 14.43 | homo-pentamer | 0.30 | HHblits | EM | NA | 0.27 | 0.93 | Zinc transport protein ZntB |
| 5n9y.1.D | 14.43 | homo-pentamer | 0.30 | HHblits | EM | NA | 0.27 | 0.93 | Zinc transport protein ZntB |
| 5n9y.1.A | 14.43 | homo-pentamer | 0.30 | HHblits | EM | NA | 0.27 | 0.93 | Zinc transport protein ZntB |
| 5n9y.1.E | 14.43 | homo-pentamer | 0.30 | HHblits | EM | NA | 0.27 | 0.93 | Zinc transport protein ZntB |
| 5n77.1.A | 16.19 | homo-pentamer | 0.30 | HHblits | X-ray | 2.80Å | 0.28 | 0.79 | Magnesium transport protein CorA |
| 4egw.1.B | 26.41 | homo-dimer | 0.06 | HHblits | X-ray | 2.50Å | 0.33 | 0.74 | Magnesium transport protein CorA |
| 4egw.1.A | 26.41 | homo-dimer | 0.06 | HHblits | X-ray | 2.50Å | 0.33 | 0.74 | Magnesium transport protein CorA |
| 3ck6.1.E | 12.55 | homo-pentamer | 0.14 | HHblits | X-ray | 1.90Å | 0.26 | 0.76 | Putative membrane transport protein |
| 3ck6.1.B | 12.55 | homo-pentamer | 0.14 | HHblits | X-ray | 1.90Å | 0.26 | 0.76 | Putative membrane transport protein |
| 3ck6.1.A | 12.55 | homo-pentamer | 0.14 | HHblits | X-ray | 1.90Å | 0.26 | 0.76 | Putative membrane transport protein |
| 3nwi.1.A | 12.50 | homo-pentamer | 0.10 | HHblits | X-ray | 3.13Å | 0.26 | 0.71 | Zinc transport protein zntB |
| 3nvo.1.A | 12.44 | homo-dimer | 0.02 | HHblits | X-ray | 2.30Å | 0.26 | 0.72 | Zinc transport protein zntB |
| 2hn1.1.A | 15.50 | homo-dimer | 0.25 | HHblits | X-ray | 2.90Å | 0.28 | 0.64 | Magnesium and cobalt transporter |
| 6v1v.1.C | 15.56 | homo-tetramer | - | HHblits | X-ray | 3.19Å | 0.28 | 0.29 | Vegetative insecticidal protein |
| 6v1v.1.D | 15.56 | homo-tetramer | - | HHblits | X-ray | 3.19Å | 0.28 | 0.29 | Vegetative insecticidal protein |
| 6yrf.1.A | 15.56 | homo-tetramer | - | HHblits | EM | NA | 0.28 | 0.29 | Vegetative insecticidal protein |
| 6v1v.1.A | 15.56 | homo-tetramer | - | HHblits | X-ray | 3.19Å | 0.28 | 0.29 | Vegetative insecticidal protein |
| 6yrf.1.B | 15.56 | homo-tetramer | - | HHblits | EM | NA | 0.28 | 0.29 | Vegetative insecticidal protein |
| 6b7n.1.A | 14.29 | homo-trimer | - | HHblits | EM | NA | 0.28 | 0.27 | Spike protein |
| 5aqt.1.B | 9.84 | monomer | - | HHblits | X-ray | 1.90Å | 0.25 | 0.19 | BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1 |
| 1t7s.1.A | 13.64 | monomer | - | HHblits | X-ray | 2.80Å | 0.28 | 0.21 | BAG-1 cochaperone |
| 1t7s.2.A | 13.64 | monomer | - | HHblits | X-ray | 2.80Å | 0.28 | 0.21 | BAG-1 cochaperone |
| 5aqf.2.B | 9.84 | monomer | - | HHblits | X-ray | 1.88Å | 0.25 | 0.19 | BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1 |
| 5aqf.1.B | 9.84 | monomer | - | HHblits | X-ray | 1.88Å | 0.25 | 0.19 | BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1 |
| 2ncj.1.A | 11.86 | monomer | - | HHblits | NMR | NA | 0.28 | 0.19 | Uncharacterized protein |
| 1hx1.1.B | 10.00 | monomer | - | HHblits | X-ray | 1.90Å | 0.25 | 0.19 | BAG family molecular chaperone regulator 1 |
| 3fzh.2.A | 10.00 | monomer | - | HHblits | X-ray | 2.00Å | 0.25 | 0.19 | BAG family molecular chaperone regulator 1 |
| 1quu.1.A | 16.95 | homo-dimer | - | HHblits | X-ray | 2.50Å | 0.28 | 0.19 | HUMAN SKELETAL MUSCLE ALPHA-ACTININ 2 |
| 6yrg.1.A | 15.56 | homo-tetramer | - | HHblits | EM | 7.00Å | 0.28 | 0.29 | Vegetative insecticidal protein |
| 5aqg.2.B | 9.84 | monomer | - | HHblits | X-ray | 2.24Å | 0.25 | 0.19 | BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1 |
| 6yrg.1.B | 15.56 | homo-tetramer | - | HHblits | EM | 7.00Å | 0.28 | 0.29 | Vegetative insecticidal protein |
The table above shows the top 50 filtered templates. A further 240 templates were found which were considered to be less suitable for modelling than the filtered list.
1i6z.1.A, 1lvf.1.A, 1lvf.2.A, 1u4q.1.A, 1u4q.2.A, 1zbt.1.A, 2bbh.1.A, 2c5i.1.B, 2iak.1.A, 2mic.1.A, 2mic.1.B, 2mjo.1.A, 2mjo.1.B, 2osz.1.C, 2osz.1.D, 2wz7.1.A, 2wz7.1.B, 2wz7.1.C, 2wz7.2.A, 2wz7.2.B, 2wz7.2.C, 2xdj.1.A, 2xdj.1.B, 2xdj.1.C, 2xdj.2.A, 2xdj.2.B, 2xdj.2.C, 2xzr.1.A, 2zjs.1.A, 2zqp.1.A, 3dl8.1.B, 3ghg.1.B, 3ghg.1.E, 3ghg.2.B, 3ghg.2.E, 3jc8.42.A, 3jc8.43.A, 3jcg.1.A, 3jcg.1.B, 3jcg.1.C, 3jcg.1.D, 3jcg.1.E, 3jch.1.A, 3jch.1.B, 3jch.1.C, 3jch.1.D, 3mk7.1.A, 3okq.1.A, 3onx.1.A, 3onx.1.B, 3pdy.1.A, 3pdy.2.A, 3pjz.1.A, 3rkg.1.A, 3stq.1.A, 3stq.1.B, 3stq.2.A, 3stq.2.B, 3stq.3.A, 3stq.4.A, 3t98.1.B, 3vpv.1.A, 3vpv.1.B, 3x29.1.A, 3zsu.1.A, 4eij.1.A, 4eij.1.B, 4h63.1.B, 4i0u.1.A, 4i0u.1.B, 4i0u.1.C, 4i0u.1.D, 4i0u.1.E, 4i0u.2.A, 4i0u.2.B, 4i0u.2.C, 4i0u.2.D, 4i0u.2.E, 4j9u.1.A, 4jo7.1.C, 4jo7.1.D, 4jo7.2.A, 4jo7.2.C, 4jo9.1.B, 4jpr.1.A, 4jq5.1.A, 4jq5.1.B, 4jq5.1.C, 4jq5.2.A, 4jq5.2.B, 4jq5.2.C, 4jq5.3.A, 4n21.1.A, 4n21.2.B, 4p79.1.A, 4v67.1.Y, 4xng.1.A, 4xng.1.B, 5aww.1.A, 5b2g.1.A, 5b2g.2.A, 5b2g.3.A, 5b2g.4.A, 5c3l.1.A, 5ch4.1.A, 5do7.1.A, 5do7.1.B, 5do7.2.A, 5do7.2.B, 5ijh.1.A, 5ijn.1.F, 5ijn.1.G, 5ijn.1.H, 5ijn.1.L, 5ijn.1.R, 5j0i.1.A, 5j1g.1.A, 5j1i.1.A, 5jrw.1.A, 5jrw.1.B, 5jrw.1.C, 5jrw.1.D, 5jtg.1.A, 5jtg.1.B, 5jtg.1.C, 5jtg.1.D, 5kte.1.A, 5kuc.1.A, 5mdy.1.G, 5n9j.1.J, 5u0p.1.C, 5u0s.1.B, 5v2s.1.A, 5xei.1.A, 5zgg.1.A, 5zgg.1.B, 5zuv.1.A, 5zuv.1.B, 5zuv.1.C, 6adq.1.D, 6ake.1.A, 6ake.2.A, 6akf.1.A, 6akf.2.A, 6akf.3.A, 6akf.4.A, 6akg.1.A, 6bm8.1.A, 6btm.1.C, 6c5l.1.Y, 6c5l.2.Y, 6d9w.1.A, 6dfp.1.A, 6dlc.1.A, 6dnc.1.c, 6eti.1.A, 6f0k.1.C, 6gap.1.A, 6gap.1.B, 6gap.1.C, 6gxn.1.r, 6hbu.1.A, 6hij.1.A, 6hwh.1.K, 6lod.1.C, 6m3p.1.B, 6m3q.1.B, 6m3r.1.B, 6n9h.1.A, 6naf.1.A, 6ncn.1.A, 6nxm.1.A, 6ny8.1.A, 6nyi.1.A, 6nyi.1.B, 6nyi.1.C, 6nyk.1.A, 6nz1.1.A, 6nz1.1.B, 6nz1.1.C, 6nz3.1.A, 6o0c.1.A, 6o0i.1.A, 6ov2.1.A, 6ov3.1.A, 6qkc.1.E, 6r17.1.A, 6r17.1.B, 6s7o.1.F, 6s7t.1.F, 6tpi.1.A, 6tqe.1.A, 6tqf.1.A, 6v4j.1.B, 6v4j.1.D, 6v4k.1.A, 6v4k.1.B, 6v4k.1.C, 6v4k.1.D, 6v4l.1.E, 6vag.1.A, 6vag.1.B, 6vja.1.A, 6vxf.1.B, 6vxh.1.B, 6vxi.1.A, 6xns.1.A, 6xns.1.B, 6xns.1.C, 6xns.2.A, 6xns.2.B, 6xns.2.C, 6xp5.1.I, 6y97.1.A, 6y97.1.B, 6y9a.1.A, 6y9a.1.B, 6ye4.1.A, 6yqf.1.A, 6yqf.1.B, 6ysl.1.A, 6ysl.1.D, 6ysl.1.E, 6ysl.1.F, 6ysl.1.G, 6z5s.1.A, 6znl.1.O, 6znl.1.V, 6zyw.1.B, 6zyw.1.C, 6zz6.1.B, 7jr7.1.A, 7jr7.1.B, 7kdp.1.A, 7kp4.1.A, 7kzm.1.Q, 7neq.1.A, 7neq.1.F, 7nez.1.A, 7nfd.1.F