SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project submitted to SWISS-MODEL workspace on April 14, 2018, 12:36 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 2018-04-12, PDB release 2018-04-06) 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
HEM;OXY;
QMEAN-1.65
-1.60
All Atom-0.14
Solvation1.17
Torsion-1.57

TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
3fh9.1.B87.67monomerHHblitsX-RAY DIFFRACTION1.62Å0.561 - 1461.00Hemoglobin beta chain

Target    VHLTDGEKNALSTAWGKVNADEVGGEALGRLLVVYPWTQRFFDSFGDLSSATAVMGNPKVKAHGKKVLDSFSNGLKHLDN
3fh9.1.B VHLSGEEKAAVTGLWGKVKVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSASAVMGNPKVKAHGKKVLDSFSEGLQHLDN

Target LKGTFASLSELHCDKLHVDPENFRLLGNVLVVVLAHHLGKEFTPQVQAAFQKVVAGVANALAHKYH
3fh9.1.B LKGTFAKLSELHCDKLHVDPENFRLLGNVLVCVLARHFGKEFTPQVQAAYQKVVAGVANALAHKYH




Materials and Methods

Template Search

Template search with BLAST and HHBlits has been performed against the SWISS-MODEL template library (SMTL, last update: 2018-04-12, last included PDB release: 2018-04-06).

The target sequence was searched with BLAST against the primary amino acid sequence contained in the SMTL. A total of 631 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 925 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.

VHLTDGEKNALSTAWGKVNADEVGGEALGRLLVVYPWTQRFFDSFGDLSSATAVMGNPKVKAHGKKVLDSFSNGLKHLDNLKGTFASLSELHCDKLHVDP
ENFRLLGNVLVVVLAHHLGKEFTPQVQAAFQKVVAGVANALAHKYH

Table T2:

TemplateSeq IdentityOligo-stateFound byScoresMethodResolutionSeq SimilarityCoverageDescription
3fh9.1.B87.67monomerHHblitsp_value=3.3e-43, score=233.7, e_value=3.7e-39, ss_score=16.3, prob=100X-ray1.62Å0.561.00Hemoglobin beta chain
3dht.1.D83.56monomerHHblitsp_value=6.3e-45, score=243.1, e_value=7.3e-41, ss_score=16.5, prob=100X-ray2.98Å0.561.00Hemoglobin subunit beta-1
2rao.1.B84.93monomerHHblitsp_value=7.1e-44, score=237, e_value=8e-40, ss_score=17, prob=100X-ray2.00Å0.561.00Hemoglobin subunit beta-1/2
3lqd.1.B84.25monomerHHblitsp_value=3.8e-44, score=238.7, e_value=4.4e-40, ss_score=16.9, prob=100X-ray2.80Å0.561.00Hemoglobin subunit beta
6hbw.1.B85.62monomerHHblitsp_value=3.2e-44, score=238.8, e_value=3.7e-40, ss_score=16.7, prob=100X-ray2.00Å0.561.00PROTEIN (HEMOGLOBIN BETA)
6hbw.1.D85.62monomerHHblitsp_value=3.2e-44, score=238.8, e_value=3.7e-40, ss_score=16.7, prob=100X-ray2.00Å0.561.00PROTEIN (HEMOGLOBIN BETA)
1k1k.1.B85.62monomerHHblitsp_value=3.1e-43, score=233.6, e_value=3.5e-39, ss_score=16.6, prob=100X-ray2.00Å0.561.00HEMOGLOBIN BETA CHAIN
1m9p.1.B85.62homo-dimerHHblitsp_value=3.1e-43, score=233.6, e_value=3.5e-39, ss_score=16.6, prob=100X-ray2.10Å0.561.00Hemoglobin beta chain
3s65.1.B85.62homo-dimerHHblitsp_value=3.1e-43, score=233.6, e_value=3.5e-39, ss_score=16.6, prob=100X-ray1.80Å0.561.00Hemoglobin subunit beta
3s65.1.D85.62homo-dimerHHblitsp_value=3.1e-43, score=233.6, e_value=3.5e-39, ss_score=16.6, prob=100X-ray1.80Å0.561.00Hemoglobin subunit beta
3hxn.1.D85.62monomerHHblitsp_value=3.9e-43, score=233.3, e_value=4.5e-39, ss_score=16.7, prob=100X-ray2.00Å0.561.00Hemoglobin subunit beta
5hy8.2.B85.62monomerHHblitsp_value=3.9e-43, score=233.3, e_value=4.5e-39, ss_score=16.7, prob=100X-ray2.30Å0.561.00Hemoglobin subunit beta
3hrw.1.B82.88monomerHHblitsp_value=2e-44, score=240.5, e_value=2.3e-40, ss_score=16.6, prob=100X-ray2.80Å0.561.00Hemoglobin subunit beta-1
3hrw.1.D82.88monomerHHblitsp_value=2e-44, score=240.5, e_value=2.3e-40, ss_score=16.6, prob=100X-ray2.80Å0.561.00Hemoglobin subunit beta-1
1jeb.1.B83.56monomerHHblitsp_value=4e-44, score=238.6, e_value=4.6e-40, ss_score=16.5, prob=100X-ray2.10Å0.561.00HEMOGLOBIN BETA-SINGLE CHAIN
4yu3.1.B84.25monomerHHblitsp_value=1.5e-44, score=240.6, e_value=1.7e-40, ss_score=16.6, prob=100X-ray2.45Å0.561.00hemoglobin
4yu4.1.D84.25monomerHHblitsp_value=1.5e-44, score=240.6, e_value=1.7e-40, ss_score=16.6, prob=100X-ray2.80Å0.561.00hemoglobin
3gou.1.D84.93monomerHHblitsp_value=2.7e-44, score=239.5, e_value=3.1e-40, ss_score=16.6, prob=100X-ray3.00Å0.561.00Hemoglobin subunit beta
3gou.1.B84.93monomerHHblitsp_value=2.7e-44, score=239.5, e_value=3.1e-40, ss_score=16.6, prob=100X-ray3.00Å0.561.00Hemoglobin subunit beta
3pel.1.B84.93monomerHHblitsp_value=2.7e-44, score=239.5, e_value=3.1e-40, ss_score=16.6, prob=100X-ray1.90Å0.561.00Hemoglobin subunit beta
4h2l.1.B80.14monomerHHblitsp_value=3.3e-43, score=233.7, e_value=3.8e-39, ss_score=17.1, prob=100X-ray1.78Å0.561.00Beta globin
5ker.1.D80.14monomerHHblitsp_value=4e-44, score=238.3, e_value=4.6e-40, ss_score=17, prob=100X-ray2.20Å0.551.00Beta globin
5ker.1.B80.14monomerHHblitsp_value=4e-44, score=238.3, e_value=4.6e-40, ss_score=17, prob=100X-ray2.20Å0.551.00Beta globin
5ker.2.D80.14monomerHHblitsp_value=4e-44, score=238.3, e_value=4.6e-40, ss_score=17, prob=100X-ray2.20Å0.551.00Beta globin
2b7h.1.B83.56monomerHHblitsp_value=3.5e-44, score=238.9, e_value=4e-40, ss_score=16.8, prob=100X-ray2.20Å0.551.00hemoglobin beta chain
1si4.1.B83.56homo-dimerHHblitsp_value=1.8e-44, score=240.7, e_value=2e-40, ss_score=16.7, prob=100X-ray2.20Å0.551.00Hemoglobin delta chain
1shr.1.D83.56homo-dimerHHblitsp_value=1.8e-44, score=240.7, e_value=2e-40, ss_score=16.7, prob=100X-ray1.88Å0.551.00Hemoglobin delta chain
4f4o.1.B84.25monomerHHblitsp_value=2.3e-44, score=240.1, e_value=2.6e-40, ss_score=16.6, prob=100X-ray2.90Å0.551.00Hemoglobin subunit beta
2pgh.1.B84.25homo-dimerHHblitsp_value=2.4e-44, score=240, e_value=2.7e-40, ss_score=16.7, prob=100X-ray2.80Å0.551.00HEMOGLOBIN (AQUO MET) (BETA CHAIN)
2pgh.1.D84.25homo-dimerHHblitsp_value=2.4e-44, score=240, e_value=2.7e-40, ss_score=16.7, prob=100X-ray2.80Å0.551.00HEMOGLOBIN (AQUO MET) (BETA CHAIN)
1qpw.1.B84.25homo-dimerHHblitsp_value=2.4e-44, score=240, e_value=2.7e-40, ss_score=16.7, prob=100X-ray1.80Å0.551.00PORCINE HEMOGLOBIN (BETA SUBUNIT)
1qpw.1.D84.25homo-dimerHHblitsp_value=2.4e-44, score=240, e_value=2.7e-40, ss_score=16.7, prob=100X-ray1.80Å0.551.00PORCINE HEMOGLOBIN (BETA SUBUNIT)
5eui.1.B82.19monomerHHblitsp_value=4.6e-44, score=238, e_value=5.2e-40, ss_score=16.9, prob=100X-ray1.45Å0.551.00HBB protein
3cy5.1.B83.45monomerHHblitsp_value=8.8e-45, score=242.1, e_value=1e-40, ss_score=16.8, prob=100X-ray2.00Å0.550.99Hemoglobin subunit beta
3gdj.1.B80.82homo-dimerHHblitsp_value=1e-43, score=236.4, e_value=1.2e-39, ss_score=16.7, prob=100X-ray2.00Å0.551.00Hemoglobin subunit beta
3cy5.1.B84.03monomerBLASTe_value=8.06261e-77, bit_score=229.18, score=583X-ray2.00Å0.560.99Hemoglobin subunit beta
2zlw.1.B80.82homo-dimerHHblitsp_value=1.8e-43, score=235.1, e_value=2e-39, ss_score=16.7, prob=100X-ray2.90Å0.541.00Hemoglobin subunit beta
1y8i.1.B80.82homo-dimerHHblitsp_value=1.8e-43, score=235.1, e_value=2e-39, ss_score=16.7, prob=100X-ray2.60Å0.541.00Hemoglobin beta chain
1y8i.1.D80.82homo-dimerHHblitsp_value=1.8e-43, score=235.1, e_value=2e-39, ss_score=16.7, prob=100X-ray2.60Å0.541.00Hemoglobin beta chain
1y8k.1.B80.82homo-dimerHHblitsp_value=1.8e-43, score=235.1, e_value=2e-39, ss_score=16.7, prob=100X-ray2.30Å0.541.00Hemoglobin beta chain
1y8h.1.B80.82monomerHHblitsp_value=1.8e-43, score=235.1, e_value=2e-39, ss_score=16.7, prob=100X-ray3.10Å0.541.00Hemoglobin beta chain
1g0b.1.B80.82monomerHHblitsp_value=1.8e-43, score=235.1, e_value=2e-39, ss_score=16.7, prob=100X-ray1.90Å0.541.00HEMOGLOBIN BETA CHAIN
2zlx.1.B80.82monomerHHblitsp_value=1.8e-43, score=235.1, e_value=2e-39, ss_score=16.7, prob=100X-ray2.80Å0.541.00Hemoglobin subunit beta
2d5x.1.B80.82monomerHHblitsp_value=1.8e-43, score=235.1, e_value=2e-39, ss_score=16.7, prob=100X-ray1.45Å0.541.00Hemoglobin beta subunit
1g08.1.B82.76monomerHHblitsp_value=1.3e-44, score=241.3, e_value=1.4e-40, ss_score=16.7, prob=100X-ray1.90Å0.550.99HEMOGLOBIN BETA CHAIN
3ciu.1.D82.76homo-dimerHHblitsp_value=1.3e-44, score=241.3, e_value=1.4e-40, ss_score=16.7, prob=100X-ray3.50Å0.550.99Hemoglobin subunit beta
2qsp.1.D82.76homo-dimerHHblitsp_value=1.3e-44, score=241.3, e_value=1.4e-40, ss_score=16.7, prob=100X-ray1.85Å0.550.99Hemoglobin subunit beta
1hda.1.B82.76monomerHHblitsp_value=1.3e-44, score=241.3, e_value=1.4e-40, ss_score=16.7, prob=100X-ray2.20Å0.550.99HEMOGLOBIN (DEOXY) (BETA CHAIN)
1fsx.1.D82.76monomerHHblitsp_value=1.3e-44, score=241.3, e_value=1.4e-40, ss_score=16.7, prob=100X-ray2.10Å0.550.99HEMOGLOBIN BETA CHAIN
1g08.1.B83.33monomerBLASTe_value=5.42652e-76, bit_score=227.254, score=578X-ray1.90Å0.550.99HEMOGLOBIN BETA CHAIN