SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project submitted to SWISS-MODEL workspace on March 15, 2018, 5:09 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 2018-03-14, PDB release 2018-03-09) 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-2.18
-0.91
All Atom-1.56
Solvation-1.47
Torsion-1.78

TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
1vgu.1.A39.81homo-dimerHHblitsX-RAY DIFFRACTION2.80Å0.371 - 2140.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

Target    MRIAAILVAGGSGSRFGSDIPKQFLPVGGKPLIRHGAERLSA-----KVDLLQPVGCADDIAPL-LQGLDHLPIVDGGKE
1vgu.1.A LDVCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGD-SRFAQLPLANHPQITVVDGGDE

Target RQDSVRAGLEALVPYAPDIVLIHDAARPYFPDHTIEDLIEALQIHD-GAIPAVPVADTLKRA--AGNIIDSTVPREGLYR
1vgu.1.A RADSVLAGLKAAGD-A-QWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWH

Target AQTPQAFKFSVLLALHR-DHP-G-GATDDAALLDQAGHSVALVPGAEDNIKVTYPADLARVERSMS
1vgu.1.A ALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLT




Materials and Methods

Template Search

Template search with BLAST and HHBlits has been performed against the SWISS-MODEL template library (SMTL, last update: 2018-03-14, last included PDB release: 2018-03-09).

The target sequence was searched with BLAST against the primary amino acid sequence contained in the SMTL. A total of 98 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 460 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.

MRIAAILVAGGSGSRFGSDIPKQFLPVGGKPLIRHGAERLSAKVDLLQPVGCADDIAPLLQGLDHLPIVDGGKERQDSVRAGLEALVPYAPDIVLIHDAA
RPYFPDHTIEDLIEALQIHDGAIPAVPVADTLKRAAGNIIDSTVPREGLYRAQTPQAFKFSVLLALHRDHPGGATDDAALLDQAGHSVALVPGAEDNIKV
TYPADLARVERSMSISMIPRIGTGYDVHAFETGRKLILCGIEVPHHQGLAGHSDADVGIHALCDAIYGALAEGDIGRHFPPTEASWKDADSARFLRHAAE
RIAARGGFLANADLTLICEKPKITPHAPAMIARLAELLGVSIDKISVKATTSEKLGFTGREEGIAAQAAVIIMIPA

Table T2:

TemplateSeq IdentityOligo-stateFound byScoresMethodResolutionSeq SimilarityCoverageDescription
1w55.1.A34.17homo-hexamerBLASTe_value=8.05578e-60, bit_score=201.445, score=511X-ray2.30Å0.370.95ISPD/ISPF BIFUNCTIONAL ENZYME
1w55.1.A32.87homo-hexamerHHblitsp_value=9e-101, score=734.1, e_value=1.1e-96, ss_score=40.2, prob=100X-ray2.30Å0.360.95ISPD/ISPF BIFUNCTIONAL ENZYME
4cvh.1.A27.16homo-dimerHHblitsp_value=1.1e-37, score=282.1, e_value=1.3e-33, ss_score=22.6, prob=100X-ray2.39Å0.330.62ISOPRENOID SYNTHASE DOMAIN-CONTAINING PROTEIN
3n9w.1.A40.57homo-dimerBLASTe_value=7.68216e-26, bit_score=105.531, score=262X-ray1.90Å0.380.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
3n9w.1.B40.57homo-dimerBLASTe_value=7.68216e-26, bit_score=105.531, score=262X-ray1.90Å0.380.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
1inj.1.A40.57homo-dimerBLASTe_value=8.36277e-26, bit_score=105.531, score=262X-ray1.55Å0.380.564-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE
1ini.1.A40.57homo-dimerBLASTe_value=8.36277e-26, bit_score=105.531, score=262X-ray1.82Å0.380.564-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE
5ddt.1.A37.74homo-dimerHHblitsp_value=8.2e-32, score=218.5, e_value=8.7e-28, ss_score=22.8, prob=100X-ray1.80Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
5hs2.1.B37.74homo-dimerHHblitsp_value=8.2e-32, score=218.5, e_value=8.7e-28, ss_score=22.8, prob=100X-ray1.90Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
5hs2.1.A37.74homo-dimerHHblitsp_value=8.2e-32, score=218.5, e_value=8.7e-28, ss_score=22.8, prob=100X-ray1.90Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
5ddv.1.A37.74homo-dimerHHblitsp_value=8.2e-32, score=218.5, e_value=8.7e-28, ss_score=22.8, prob=100X-ray2.30Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
2xwm.1.A37.91homo-dimerBLASTe_value=3.82054e-24, bit_score=100.523, score=249X-ray1.80Å0.380.562-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
2xwm.1.B37.91homo-dimerBLASTe_value=3.82054e-24, bit_score=100.523, score=249X-ray1.80Å0.380.562-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
2xwl.1.B37.91homo-dimerBLASTe_value=3.82054e-24, bit_score=100.523, score=249X-ray1.49Å0.380.562-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
1vgt.1.A43.48homo-dimerBLASTe_value=7.8774e-26, bit_score=105.531, score=262X-ray1.80Å0.390.552-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
1vgt.1.B43.48homo-dimerBLASTe_value=7.8774e-26, bit_score=105.531, score=262X-ray1.80Å0.390.552-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
1vgu.1.A43.48homo-dimerBLASTe_value=7.8774e-26, bit_score=105.531, score=262X-ray2.80Å0.390.552-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
1vgu.1.B43.48homo-dimerBLASTe_value=7.8774e-26, bit_score=105.531, score=262X-ray2.80Å0.390.552-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
3n9w.1.A39.81homo-dimerHHblitsp_value=4.3e-34, score=233.2, e_value=4.5e-30, ss_score=23.2, prob=100X-ray1.90Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
3n9w.1.B39.81homo-dimerHHblitsp_value=4.3e-34, score=233.2, e_value=4.5e-30, ss_score=23.2, prob=100X-ray1.90Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
1inj.1.A39.81homo-dimerHHblitsp_value=1.1e-33, score=231.9, e_value=1.2e-29, ss_score=22.9, prob=100X-ray1.55Å0.370.564-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE
1ini.1.A39.81homo-dimerHHblitsp_value=1.1e-33, score=231.9, e_value=1.2e-29, ss_score=22.9, prob=100X-ray1.82Å0.370.564-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE
1vgt.1.A39.81homo-dimerHHblitsp_value=1e-33, score=232, e_value=1.1e-29, ss_score=23.2, prob=100X-ray1.80Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
1vgt.1.B39.81homo-dimerHHblitsp_value=1e-33, score=232, e_value=1.1e-29, ss_score=23.2, prob=100X-ray1.80Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
1vgu.1.A39.81homo-dimerHHblitsp_value=1e-33, score=232, e_value=1.1e-29, ss_score=23.2, prob=100X-ray2.80Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
1vgu.1.B39.81homo-dimerHHblitsp_value=1e-33, score=232, e_value=1.1e-29, ss_score=23.2, prob=100X-ray2.80Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
1h3m.1.A43.00homo-dimerBLASTe_value=2.26066e-25, bit_score=104.375, score=259X-ray2.40Å0.390.552-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
5ddt.1.A37.91homo-dimerBLASTe_value=1.80415e-28, bit_score=113.235, score=282X-ray1.80Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
5hs2.1.B37.91homo-dimerBLASTe_value=1.80415e-28, bit_score=113.235, score=282X-ray1.90Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
5hs2.1.A37.91homo-dimerBLASTe_value=1.80415e-28, bit_score=113.235, score=282X-ray1.90Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
5ddv.1.A37.91homo-dimerBLASTe_value=1.80415e-28, bit_score=113.235, score=282X-ray2.30Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
4ys8.1.A37.56monomerHHblitsp_value=3.8e-34, score=234.8, e_value=3.9e-30, ss_score=24.3, prob=100X-ray2.45Å0.360.572-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
4zdq.1.A37.56monomerHHblitsp_value=3.8e-34, score=234.8, e_value=3.9e-30, ss_score=24.3, prob=100X-ray2.30Å0.360.572-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
2xwm.1.A36.49homo-dimerHHblitsp_value=2.8e-33, score=226.4, e_value=2.9e-29, ss_score=23.6, prob=100X-ray1.80Å0.370.562-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
2xwm.1.B36.49homo-dimerHHblitsp_value=2.8e-33, score=226.4, e_value=2.9e-29, ss_score=23.6, prob=100X-ray1.80Å0.370.562-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
2xwl.1.B36.49homo-dimerHHblitsp_value=2.8e-33, score=226.4, e_value=2.9e-29, ss_score=23.6, prob=100X-ray1.49Å0.370.562-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
5mro.1.A33.18homo-dimerBLASTe_value=2.12792e-23, bit_score=98.2117, score=243X-ray1.80Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
5mrn.1.A33.18homo-dimerBLASTe_value=2.12792e-23, bit_score=98.2117, score=243X-ray2.00Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
2ycm.1.A33.18homo-dimerBLASTe_value=2.76428e-23, bit_score=97.8265, score=242X-ray1.80Å0.370.562-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
4nak.1.B33.18homo-dimerBLASTe_value=3.40683e-23, bit_score=97.8265, score=242X-ray1.80Å0.370.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
2yc3.1.A33.18homo-dimerBLASTe_value=3.40683e-23, bit_score=97.8265, score=242X-ray1.40Å0.370.562-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
1w77.1.A33.18homo-dimerBLASTe_value=4.45922e-23, bit_score=97.4413, score=241X-ray2.00Å0.360.562C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
4nai.1.A33.18homo-dimerBLASTe_value=4.45922e-23, bit_score=97.4413, score=241X-ray1.50Å0.360.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
4ys8.1.A42.44monomerBLASTe_value=5.54103e-29, bit_score=114.775, score=286X-ray2.45Å0.390.552-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
4zdq.1.A42.44monomerBLASTe_value=5.54103e-29, bit_score=114.775, score=286X-ray2.30Å0.390.552-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
5mrq.1.A32.70homo-dimerBLASTe_value=4.3506e-22, bit_score=94.3597, score=233X-ray2.20Å0.360.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
3okr.1.A33.02homo-dimerHHblitsp_value=1.1e-33, score=231, e_value=1.1e-29, ss_score=24, prob=100X-ray2.40Å0.360.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
3okr.1.B33.02homo-dimerHHblitsp_value=1.1e-33, score=231, e_value=1.1e-29, ss_score=24, prob=100X-ray2.40Å0.360.562-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
3f1c.1.A30.33homo-dimerHHblitsp_value=1.8e-31, score=218, e_value=1.9e-27, ss_score=22.8, prob=100X-ray2.30Å0.360.56Putative 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2
4jis.1.A30.95homo-dimerHHblitsp_value=5.4e-32, score=222.2, e_value=5.7e-28, ss_score=22.8, prob=100X-ray1.77Å0.370.56ribitol-5-phosphate cytidylyltransferase