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 10, 2018, 12:52 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:

Results

The SWISS-MODEL template library (SMTL version 2018-04-04, PDB release 2018-03-29) 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
PDBProMod3Homo-2-mer
QMEAN-1.43
-1.41
All Atom-1.92
Solvation-0.71
Torsion-1.01

TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
3tqu.1.A38.33homo-dimerBLASTX-RAY DIFFRACTION1.90Å0.396 - 1880.91Non-canonical purine NTP pyrophosphatase

Target    LAFASGSDHKTKEMQMLLSPFGYEIVTPKILGIPFSPEETESTFVGNSFIKSKELFRLTGFPSFADDSGISVDALGGEPG
3tqu.1.A IVLASQNSSKLAEMQELLRDLEIKFIPQTEFSVP-DIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPG

Target VLSARFGGPGLSDKDRALYLLNKL--GTNHNRKAHYSCVVSFVDANHQ---VSFEGKVEGLIASDYDELGKFGFGYDPIF
3tqu.1.A VFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALMENENDPAPLICHGVWEGEIA--REPRGKNGFGYDPIF

Target YYPEFGKRFSEVPEGEKNKVSHRKKAME
3tqu.1.A YVPSHQRTAAELDPQEKNAISHRGQALE




Materials and Methods

Template Search

Template search with BLAST and HHBlits has been performed against the SWISS-MODEL template library (SMTL, last update: 2018-04-04, last included PDB release: 2018-03-29).

The target sequence was searched with BLAST against the primary amino acid sequence contained in the SMTL. A total of 20 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 213 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.

MTKKTLAFASGSDHKTKEMQMLLSPFGYEIVTPKILGIPFSPEETESTFVGNSFIKSKELFRLTGFPSFADDSGISVDALGGEPGVLSARFGGPGLSDKD
RALYLLNKLGTNHNRKAHYSCVVSFVDANHQVSFEGKVEGLIASDYDELGKFGFGYDPIFYYPEFGKRFSEVPEGEKNKVSHRKKAMELFLEWFQTIQ

Table T2:

TemplateSeq IdentityOligo-stateFound byScoresMethodResolutionSeq SimilarityCoverageDescription
1k7k.1.A36.65monomerHHblitsp_value=2.3e-75, score=468.8, e_value=2.7e-71, ss_score=24.6, prob=100X-ray1.50Å0.380.96Hypothetical protein yggV
1k7k.1.A37.04monomerBLASTe_value=9.53091e-35, bit_score=125.561, score=314X-ray1.50Å0.390.95Hypothetical protein yggV
2pyu.1.A36.13homo-dimerHHblitsp_value=2.1e-75, score=468.5, e_value=2.5e-71, ss_score=24.3, prob=100X-ray2.02Å0.380.96Inosine Triphosphate Pyrophosphatase RdgB
2q16.1.B36.13homo-dimerHHblitsp_value=2.1e-75, score=468.5, e_value=2.5e-71, ss_score=24.3, prob=100X-ray1.95Å0.380.96HAM1 protein homolog
2q16.1.A36.13homo-dimerHHblitsp_value=2.1e-75, score=468.5, e_value=2.5e-71, ss_score=24.3, prob=100X-ray1.95Å0.380.96HAM1 protein homolog
2pyu.1.A36.51homo-dimerBLASTe_value=1.09429e-33, bit_score=122.865, score=307X-ray2.02Å0.390.95Inosine Triphosphate Pyrophosphatase RdgB
2q16.1.B36.51homo-dimerBLASTe_value=1.09429e-33, bit_score=122.865, score=307X-ray1.95Å0.390.95HAM1 protein homolog
2q16.1.A36.51homo-dimerBLASTe_value=1.09429e-33, bit_score=122.865, score=307X-ray1.95Å0.390.95HAM1 protein homolog
3tqu.1.A36.13homo-dimerHHblitsp_value=9.6e-77, score=471.5, e_value=1.1e-72, ss_score=24.1, prob=100X-ray1.90Å0.380.96Non-canonical purine NTP pyrophosphatase
4bnq.1.A36.70homo-dimerBLASTe_value=1.55046e-32, bit_score=119.013, score=297X-ray2.28Å0.380.95NON-CANONICAL PURINE NTP PYROPHOSPHATASE
4bnq.1.B36.70homo-dimerBLASTe_value=1.55046e-32, bit_score=119.013, score=297X-ray2.28Å0.380.95NON-CANONICAL PURINE NTP PYROPHOSPHATASE
4bnq.1.A35.98homo-dimerHHblitsp_value=2.3e-72, score=441.1, e_value=2.6e-68, ss_score=24.1, prob=100X-ray2.28Å0.380.95NON-CANONICAL PURINE NTP PYROPHOSPHATASE
4bnq.1.B35.98homo-dimerHHblitsp_value=2.3e-72, score=441.1, e_value=2.6e-68, ss_score=24.1, prob=100X-ray2.28Å0.380.95NON-CANONICAL PURINE NTP PYROPHOSPHATASE
1vp2.1.A39.34homo-tetramerBLASTe_value=3.00481e-23, bit_score=94.7449, score=234X-ray1.78Å0.390.92Putative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog
1vp2.1.A34.95homo-tetramerHHblitsp_value=5.6e-78, score=481.1, e_value=6.6e-74, ss_score=23.1, prob=100X-ray1.78Å0.370.94Putative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog
3tqu.1.A38.33homo-dimerBLASTe_value=5.18121e-33, bit_score=120.553, score=301X-ray1.90Å0.390.91Non-canonical purine NTP pyrophosphatase
4f95.1.A30.43homo-dimerBLASTe_value=3.72025e-11, bit_score=60.077, score=144X-ray2.07Å0.340.93Inosine triphosphate pyrophosphatase
2j4e.1.A30.43homo-dimerBLASTe_value=3.97834e-11, bit_score=60.077, score=144X-ray2.80Å0.340.93INOSINE TRIPHOSPHATE PYROPHOSPHATASE
2car.1.A30.43homo-dimerBLASTe_value=3.97834e-11, bit_score=60.077, score=144X-ray1.09Å0.340.93INOSINE TRIPHOSPHATE PYROPHOSPHATASE
2j4e.5.B30.43homo-dimerBLASTe_value=3.97834e-11, bit_score=60.077, score=144X-ray2.80Å0.340.93INOSINE TRIPHOSPHATE PYROPHOSPHATASE
2i5d.1.A30.43homo-dimerBLASTe_value=4.36459e-11, bit_score=59.6918, score=143X-ray1.63Å0.340.93inosine triphosphate pyrophosphohydrolase
1b78.1.A30.77homo-dimerHHblitsp_value=3.9e-74, score=452.5, e_value=4.6e-70, ss_score=21, prob=100X-ray2.20Å0.350.92PYROPHOSPHATASE
1b78.1.B30.77homo-dimerHHblitsp_value=3.9e-74, score=452.5, e_value=4.6e-70, ss_score=21, prob=100X-ray2.20Å0.350.92PYROPHOSPHATASE
2e5x.1.A34.09homo-dimerBLASTe_value=4.90565e-16, bit_score=73.9442, score=180X-ray2.00Å0.370.89Hypothetical protein PH1917
2zti.1.A34.09homo-dimerBLASTe_value=7.12227e-16, bit_score=73.559, score=179X-ray2.60Å0.370.89NTPASE
2dvn.1.A34.09homo-dimerBLASTe_value=7.12227e-16, bit_score=73.559, score=179X-ray1.60Å0.370.89Hypothetical protein PH1917
2dvn.1.B34.09homo-dimerBLASTe_value=7.12227e-16, bit_score=73.559, score=179X-ray1.60Å0.370.89Hypothetical protein PH1917
2dvp.1.A34.09homo-dimerBLASTe_value=7.12227e-16, bit_score=73.559, score=179X-ray1.90Å0.370.89Hypothetical protein PH1917
2e5x.1.A29.12homo-dimerHHblitsp_value=5.3e-77, score=467.5, e_value=6.1e-73, ss_score=21, prob=100X-ray2.00Å0.330.92Hypothetical protein PH1917
2zti.1.A29.12homo-dimerHHblitsp_value=1.1e-75, score=459.4, e_value=1.3e-71, ss_score=20.8, prob=100X-ray2.60Å0.330.92NTPASE
2dvn.1.A29.12homo-dimerHHblitsp_value=1.1e-75, score=459.4, e_value=1.3e-71, ss_score=20.8, prob=100X-ray1.60Å0.330.92Hypothetical protein PH1917
2dvn.1.B29.12homo-dimerHHblitsp_value=1.1e-75, score=459.4, e_value=1.3e-71, ss_score=20.8, prob=100X-ray1.60Å0.330.92Hypothetical protein PH1917
2dvp.1.A29.12homo-dimerHHblitsp_value=1.1e-75, score=459.4, e_value=1.3e-71, ss_score=20.8, prob=100X-ray1.90Å0.330.92Hypothetical protein PH1917
1b78.1.A32.57homo-dimerBLASTe_value=2.23664e-17, bit_score=78.1814, score=191X-ray2.20Å0.360.88PYROPHOSPHATASE
1b78.1.B32.57homo-dimerBLASTe_value=2.23664e-17, bit_score=78.1814, score=191X-ray2.20Å0.360.88PYROPHOSPHATASE
4f95.1.A27.07homo-dimerHHblitsp_value=3.4e-72, score=442.1, e_value=3.9e-68, ss_score=20.3, prob=100X-ray2.07Å0.330.91Inosine triphosphate pyrophosphatase
2j4e.1.A26.52homo-dimerHHblitsp_value=6.7e-72, score=440, e_value=7.8e-68, ss_score=20.6, prob=100X-ray2.80Å0.330.91INOSINE TRIPHOSPHATE PYROPHOSPHATASE
2car.1.A26.52homo-dimerHHblitsp_value=6.7e-72, score=440, e_value=7.8e-68, ss_score=20.6, prob=100X-ray1.09Å0.330.91INOSINE TRIPHOSPHATE PYROPHOSPHATASE
2j4e.5.B26.52homo-dimerHHblitsp_value=6.7e-72, score=440, e_value=7.8e-68, ss_score=20.6, prob=100X-ray2.80Å0.330.91INOSINE TRIPHOSPHATE PYROPHOSPHATASE
2i5d.1.A26.11homo-dimerHHblitsp_value=2.7e-71, score=436.6, e_value=3.1e-67, ss_score=20.8, prob=100X-ray1.63Å0.330.91inosine triphosphate pyrophosphohydrolase
4p0e.1.A20.56monomerHHblitsp_value=9.6e-06, score=39.9, e_value=0.11, ss_score=14.5, prob=96X-ray2.30Å0.300.54Maf-like protein YhdE
4p0e.1.B20.56monomerHHblitsp_value=9.6e-06, score=39.9, e_value=0.11, ss_score=14.5, prob=96X-ray2.30Å0.300.54Maf-like protein YhdE
1exc.1.B22.02monomerHHblitsp_value=6.8e-06, score=40.8, e_value=0.08, ss_score=14.7, prob=96.3X-ray2.70Å0.290.55PROTEIN MAF
1ex2.1.A22.02monomerHHblitsp_value=6.8e-06, score=40.8, e_value=0.08, ss_score=14.7, prob=96.3X-ray1.85Å0.290.55PROTEIN MAF
1exc.1.A22.02monomerHHblitsp_value=6.8e-06, score=40.8, e_value=0.08, ss_score=14.7, prob=96.3X-ray2.70Å0.290.55PROTEIN MAF
1ex2.1.B22.02monomerHHblitsp_value=6.8e-06, score=40.8, e_value=0.08, ss_score=14.7, prob=96.3X-ray1.85Å0.290.55PROTEIN MAF
4p0u.1.A19.81monomerHHblitsp_value=3.7e-05, score=36.4, e_value=0.44, ss_score=13.9, prob=94.7X-ray2.36Å0.300.54Maf-like protein YceF
4heb.1.A21.50monomerHHblitsp_value=2.7e-05, score=38, e_value=0.33, ss_score=14.4, prob=95.1X-ray2.26Å0.290.54Septum formation protein Maf
2l69.1.A15.87monomerHHblitsp_value=0.00014, score=31.5, e_value=1.9, ss_score=2.2, prob=62NMRNA0.300.32Rossmann 2x3 fold protein
2lrh.1.A11.29monomerHHblitsp_value=8e-05, score=32.7, e_value=1.2, ss_score=2.5, prob=71.3NMRNA0.280.31De novo designed protein