SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project submitted to SWISS-MODEL workspace on Aug. 17, 2017, 11:20 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:

Results

The SWISS-MODEL template library (SMTL version 2017-08-09, PDB release 2017-08-04) was searched with BLAST (Camacho et al.) and HHBlits (Remmert et al.) for evolutionary related structures matching the target sequence in Table T1. For details on the template search, see Materials and Methods. Overall 50 templates were found (Table T2).

Models

The following model was built (see Materials and Methods "Model Building"):

FileBuilt withOligo-StateLigandsQMEAN
PDBProMod3Monomer
QMEAN-1.38
0.35
All Atom0.67
Solvation0.47
Torsion-1.51

TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
2v7y.1.A66.99MONOMERBLASTX-RAY DIFFRACTION2.37Å0.491 - 5350.79CHAPERONE PROTEIN DNAK

Target    MAKIIGIDLGTTNSCVAVMENNKPKVIENAEGTRTTPSIVAYAEDNEVLVGASAKRQAVTNPENTLFAIKRLIGRKFDEE
2v7y.1.A MSKIIGIDLGTTNSCVAVLEGGEVKVIPNPEGNRTTPSVVAF-KNGERLVGEVAKRQAITNP-NTIISIKRHMG------

Target VVQKDISVTPYKIVRADNNDAWIEVRGRKIAPPEVSAQVLMKMKKTAEDYLGESVTEAVITVPAYFNDSQRQATKDAGRI
2v7y.1.A --------TDYKV----------EIEGKQYTPQEISAIILQYLKSYAEDYLGEPVTRAVITVPAYFNDAQRQATKDAGRI

Target AGLEVKRIINEPTAAALAFGMDKKEGDRKIAVYDLGGGTFDISIIEIAEIEGEHQFEVLATNGDTFLGGEDFDSSVISYL
2v7y.1.A AGLEVERIINEPTAAALAYGLDKEE-DQTILVYDLGGGTFDVSILELGDGV----FEVKATAGDNHLGGDDFDQVIIDYL

Target VEEFRKESGIDLKKDMLALQRLKDAAEKAKIELSSSQQTEVNLPYITADASGPKHLAVKITRAKLESLVEELIERTAGPC
2v7y.1.A VNQFKQEHGIDLSKDKMALQRLKDAAEKAKKELSGVTQTQISLPFISANENGPLHLEMTLTRAKFEELSAHLVERTMGPV

Target RTALKDAGLSVSDIDDVILVGGQTRMPKVQDKVKEIFGKEPRKDVNPDEAVAIGAAIQGGVLQGDVKDVLLLDVTPLSLG
2v7y.1.A RQALQDAGLTPADIDKVILVGGSTRIPAVQEAIKRELGKEPHKGVNPDEVVAIGAAIQGGVIAGEVKDVVLLDVTPLSLG

Target IETLGGVMTKLIQKNTTIPTKAQQIFSTAEDSQTAVTIHVLQGEREMASGNKSLGQFNLTDIPPAQRGMPQIEVTFDIDA
2v7y.1.A IETMGGVFTKLIERNTTIPTSKSQVFTTAADNQTTVDIHVLQGERPMAADNKSLGRFQLTGIPPAPRGVPQIEVTFDIDA

Target NGILHVSAKDKATGKENKIKIQASSGLSEDEIQKMVKDAETHAEEDKKALELVNS
2v7y.1.A NGIVHVRAKDLGTNKEQSITIKSSSGLSEEEIQRMIKEAEENAEADRKRKEAAEL




Materials and Methods

Template Search

Template search with BLAST and HHBlits has been performed against the SWISS-MODEL template library (SMTL, last update: 2017-08-09, last included PDB release: 2017-08-04).

The target sequence was searched with BLAST against the primary amino acid sequence contained in the SMTL. A total of 165 templates were found.

An initial HHblits profile has been built using the procedure outlined in (Remmert et al.), followed by 1 iteration of HHblits against NR20. The obtained profile has then be searched against all profiles of the SMTL. A total of 1013 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. 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. In case loop modelling with ProMod3 fails, an alternative model is built with PROMOD-II (Guex et al.).

Model Quality Estimation

The global and per-residue model quality has been assessed using the QMEAN scoring function (Benkert et al.) . For improved performance, weights of the individual QMEAN terms have been trained specifically for SWISS-MODEL.

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

Table T1:

Primary amino acid sequence for which templates were searched and models were built.

MAKIIGIDLGTTNSCVAVMENNKPKVIENAEGTRTTPSIVAYAEDNEVLVGASAKRQAVTNPENTLFAIKRLIGRKFDEEVVQKDISVTPYKIVRADNND
AWIEVRGRKIAPPEVSAQVLMKMKKTAEDYLGESVTEAVITVPAYFNDSQRQATKDAGRIAGLEVKRIINEPTAAALAFGMDKKEGDRKIAVYDLGGGTF
DISIIEIAEIEGEHQFEVLATNGDTFLGGEDFDSSVISYLVEEFRKESGIDLKKDMLALQRLKDAAEKAKIELSSSQQTEVNLPYITADASGPKHLAVKI
TRAKLESLVEELIERTAGPCRTALKDAGLSVSDIDDVILVGGQTRMPKVQDKVKEIFGKEPRKDVNPDEAVAIGAAIQGGVLQGDVKDVLLLDVTPLSLG
IETLGGVMTKLIQKNTTIPTKAQQIFSTAEDSQTAVTIHVLQGEREMASGNKSLGQFNLTDIPPAQRGMPQIEVTFDIDANGILHVSAKDKATGKENKIK
IQASSGLSEDEIQKMVKDAETHAEEDKKALELVNSRNQCDAMIHSVKKSLTEYGDKLEADEKSKIEAALKDAEEALKSGDKEAIDAKTQVLTEASHKLAE
KMYAQEQAQAGQQAGPGAGSASAGQSGEKPVEGEVVDAEFEEVKDKK

Table T2:

TemplateSeq IdentityOligo-stateFound byScoresMethodResolutionSeq SimilarityCoverageDescription
2kho.1.A74.96monomerHHblitsp_value=1e-109, score=914.7, e_value=2e-105, ss_score=79.5, prob=100NMRNA0.520.93Heat shock protein 70
2kho.1.A75.50monomerBLASTe_value=0, bit_score=862.448, score=2227NMRNA0.520.93Heat shock protein 70
4b9q.1.A74.63monomerHHblitsp_value=2e-111, score=930.9, e_value=2e-107, ss_score=79.8, prob=100X-ray2.40Å0.520.93CHAPERONE PROTEIN DNAK
4b9q.1.A75.17monomerBLASTe_value=0, bit_score=858.981, score=2218X-ray2.40Å0.520.93CHAPERONE PROTEIN DNAK
4jn4.1.A74.04homo-dimerHHblitsp_value=5e-107, score=894.9, e_value=5e-103, ss_score=79.8, prob=100X-ray2.30Å0.510.93Chaperone protein DnaK
4jn4.1.A74.96homo-dimerBLASTe_value=0, bit_score=841.262, score=2172X-ray2.30Å0.520.92Chaperone protein DnaK
5e84.3.A51.96monomerHHblitsp_value=7e-103, score=859.9, e_value=7.8e-99, ss_score=76, prob=100X-ray2.99Å0.440.9178 kDa glucose-regulated protein
5e84.1.A51.96monomerHHblitsp_value=7e-103, score=859.9, e_value=7.8e-99, ss_score=76, prob=100X-ray2.99Å0.440.9178 kDa glucose-regulated protein
5fpn.1.A49.24monomerHHblitsp_value=1e-106, score=896.5, e_value=1e-102, ss_score=79.3, prob=100X-ray1.96Å0.430.92HEAT SHOCK-RELATED 70 KDA PROTEIN 2
5e84.1.A53.19monomerBLASTe_value=1.36817e-177, bit_score=523.087, score=1346X-ray2.99Å0.450.8578 kDa glucose-regulated protein
5e84.3.A53.19monomerBLASTe_value=1.36817e-177, bit_score=523.087, score=1346X-ray2.99Å0.450.8578 kDa glucose-regulated protein
4ani.1.D66.99hetero-oligomerBLASTe_value=0, bit_score=624.78, score=1610X-ray4.09Å0.490.79CHAPERONE PROTEIN DNAK
4ani.1.G66.99hetero-oligomerBLASTe_value=0, bit_score=624.78, score=1610X-ray4.09Å0.490.79CHAPERONE PROTEIN DNAK
4ani.1.H66.99hetero-oligomerBLASTe_value=0, bit_score=624.78, score=1610X-ray4.09Å0.490.79CHAPERONE PROTEIN DNAK
2v7y.1.A66.99monomerBLASTe_value=0, bit_score=624.78, score=1610X-ray2.37Å0.490.79CHAPERONE PROTEIN DNAK
4ani.1.C66.99hetero-oligomerBLASTe_value=0, bit_score=624.78, score=1610X-ray4.09Å0.490.79CHAPERONE PROTEIN DNAK
1yuw.1.A53.23monomerHHblitsp_value=7.5e-95, score=784.7, e_value=8.3e-91, ss_score=70.3, prob=100X-ray2.60Å0.450.84Heat shock cognate 71 kDa protein
4fl9.1.A53.23monomerHHblitsp_value=7.5e-95, score=784.7, e_value=8.3e-91, ss_score=70.3, prob=100X-ray1.90Å0.450.84Heat shock cognate 71 kDa protein
3c7n.1.B53.33hetero-oligomerHHblitsp_value=8.4e-95, score=784.3, e_value=9.4e-91, ss_score=70.5, prob=100X-ray3.12Å0.450.83Heat shock cognate
1yuw.1.A54.38monomerBLASTe_value=5.80701e-175, bit_score=514.612, score=1324X-ray2.60Å0.450.83Heat shock cognate 71 kDa protein
4fl9.1.A54.38monomerBLASTe_value=5.80701e-175, bit_score=514.612, score=1324X-ray1.90Å0.450.83Heat shock cognate 71 kDa protein
3c7n.1.B54.19hetero-oligomerBLASTe_value=9.44858e-175, bit_score=513.842, score=1322X-ray3.12Å0.450.83Heat shock cognate
2v7y.1.A66.21monomerHHblitsp_value=3.1e-91, score=747.2, e_value=3.5e-87, ss_score=67.2, prob=100X-ray2.37Å0.490.79CHAPERONE PROTEIN DNAK
4ani.1.C66.21hetero-oligomerHHblitsp_value=3.1e-91, score=747.2, e_value=3.5e-87, ss_score=67.2, prob=100X-ray4.09Å0.490.79CHAPERONE PROTEIN DNAK
4ani.1.D66.21hetero-oligomerHHblitsp_value=3.1e-91, score=747.2, e_value=3.5e-87, ss_score=67.2, prob=100X-ray4.09Å0.490.79CHAPERONE PROTEIN DNAK
4rtf.1.A62.89monomerHHblitsp_value=4.6e-92, score=761.2, e_value=5.1e-88, ss_score=66, prob=100X-ray2.77Å0.480.79Chaperone protein DnaK
5fpn.1.A53.07monomerBLASTe_value=4.4854e-169, bit_score=502.671, score=1293X-ray1.96Å0.450.83HEAT SHOCK-RELATED 70 KDA PROTEIN 2
4rtf.1.A62.89monomerBLASTe_value=0, bit_score=601.282, score=1549X-ray2.77Å0.480.79Chaperone protein DnaK
2v7z.1.A54.06monomerHHblitsp_value=2.1e-93, score=771.2, e_value=2.4e-89, ss_score=67.7, prob=100X-ray3.50Å0.450.82HEAT SHOCK COGNATE 71 KDA PROTEIN
2v7z.2.A54.06monomerHHblitsp_value=2.1e-93, score=771.2, e_value=2.4e-89, ss_score=67.7, prob=100X-ray3.50Å0.450.82HEAT SHOCK COGNATE 71 KDA PROTEIN
1dkg.1.C77.43hetero-oligomerHHblitsp_value=3.1e-57, score=451.8, e_value=3.3e-53, ss_score=49.3, prob=100X-ray2.80Å0.530.59MOLECULAR CHAPERONE DNAK
1dkg.1.C77.24hetero-oligomerBLASTe_value=0, bit_score=580.482, score=1495X-ray2.80Å0.530.57MOLECULAR CHAPERONE DNAK
4kbo.1.A66.67monomerHHblitsp_value=8.5e-57, score=449.1, e_value=9.1e-53, ss_score=49.1, prob=100X-ray2.80Å0.500.58Stress-70 protein, mitochondrial
4j8f.1.A49.87homo-dimerHHblitsp_value=6.9e-56, score=462.9, e_value=7.4e-52, ss_score=49.1, prob=100X-ray2.70Å0.430.61Heat shock 70 kDa protein 1A/1B, Hsc70-interacting protein
4kbo.1.A65.93monomerBLASTe_value=2.42171e-168, bit_score=491.115, score=1263X-ray2.80Å0.500.56Stress-70 protein, mitochondrial
3iuc.1.A53.46homo-dimerHHblitsp_value=6.2e-56, score=447.5, e_value=6.8e-52, ss_score=48.8, prob=100X-ray2.40Å0.450.58Heat shock 70kDa protein 5 (Glucose-regulated protein, 78kDa)
3ldp.1.A53.33monomerHHblitsp_value=5e-58, score=459.7, e_value=5.4e-54, ss_score=48.3, prob=100X-ray2.20Å0.450.5878 kDa glucose-regulated protein
3ldo.1.A53.33monomerHHblitsp_value=5e-58, score=459.7, e_value=5.4e-54, ss_score=48.3, prob=100X-ray1.95Å0.450.5878 kDa glucose-regulated protein
5ey4.2.A53.33monomerHHblitsp_value=2e-58, score=465.9, e_value=2.2e-54, ss_score=48.8, prob=100X-ray1.86Å0.450.5878 kDa glucose-regulated protein
3qml.2.A52.82hetero-oligomerHHblitsp_value=7.5e-55, score=435.4, e_value=8.2e-51, ss_score=48.3, prob=100X-ray2.31Å0.450.5878 kDa glucose-regulated protein homolog
3qml.1.A52.82hetero-oligomerHHblitsp_value=7.5e-55, score=435.4, e_value=8.2e-51, ss_score=48.3, prob=100X-ray2.31Å0.450.5878 kDa glucose-regulated protein homolog
3qfp.1.A52.82monomerHHblitsp_value=7.5e-55, score=435.4, e_value=8.2e-51, ss_score=48.3, prob=100X-ray2.26Å0.450.5878 kDa glucose-regulated protein homolog
3qfu.1.A52.82monomerHHblitsp_value=1.6e-55, score=440.9, e_value=1.7e-51, ss_score=48.4, prob=100X-ray1.80Å0.450.5878 kDa glucose-regulated protein homolog
3fe1.1.A52.67monomerHHblitsp_value=2.7e-56, score=449.6, e_value=3e-52, ss_score=48.6, prob=100X-ray2.20Å0.440.58Heat shock 70 kDa protein 6
5bn9.1.A51.60monomerHHblitsp_value=2.2e-56, score=446.7, e_value=2.4e-52, ss_score=48.1, prob=100X-ray1.69Å0.440.58Heat shock 70 kDa protein 1A
3l6q.1.A52.14monomerHHblitsp_value=2e-57, score=458.1, e_value=2.2e-53, ss_score=48.2, prob=100X-ray2.29Å0.440.58Heat shock 70 (HSP70) protein
3kvg.1.A52.14monomerHHblitsp_value=2e-57, score=458.1, e_value=2.2e-53, ss_score=48.2, prob=100X-ray2.15Å0.440.58Heat shock 70 (HSP70) protein
5bpn.1.A51.34monomerHHblitsp_value=7.5e-56, score=442.6, e_value=8.1e-52, ss_score=47.7, prob=100X-ray2.10Å0.440.58Heat shock 70 kDa protein 1A
5bpm.1.A51.34monomerHHblitsp_value=7.5e-56, score=442.6, e_value=8.1e-52, ss_score=47.7, prob=100X-ray1.83Å0.440.58Heat shock 70 kDa protein 1A
3gdq.1.A51.07monomerHHblitsp_value=2.8e-57, score=458.5, e_value=3e-53, ss_score=48.3, prob=100X-ray1.80Å0.440.58Heat shock 70 kDa protein 1-like