SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "SODC_DROME P61851 Superoxide dismutase [Cu-Zn]" submitted to SWISS-MODEL workspace on Jan. 11, 2024, 2 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 2023-12-24, PDB release 2023-12-15) was searched with for evolutionary related structures matching the target sequence in Table T1. For details on the template search, see Materials and Methods. Overall 489 templates were found (Table T2).

Models

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

Model #01

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.4.0 homo-dimer (matching prediction)
2 x CU: COPPER (II) ION;
2 x ZN: ZINC ION;
0.88 0.85 ± 0.05
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
3l9y.1.A 67.97 homo-dimer 0.92 HHblits X-ray 1.80Å 0.51 2 - 153 1.00 Superoxide dismutase [Cu-Zn]

Included Ligands

Ligand Description
2 x CU
COPPER (II) ION
2 x ZN
ZINC ION

Target    MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGLAKGLHGFHVHEFGDNTNGCMSSGPHFNPYGKEHGAPVDENRHL
3l9y.1.A MPAKAVCVLRGDVSGTVFFDQQDEKSPVVVSGEVQGLTKGKHGFHVHEFGDNTNGCTSAGAHFNPEKQDHGGPSSAVRHV

Target GDLGNIEATGD-CPTKVNITDSKITLFGADSIIGRTVVVHADADDLGQGGHELSKSTGNAGARIGCGVIGIAKV
3l9y.1.A GDLGNIEAIEDAGVTKVSIQDSQISLHGPNSIIGRTLVVHADPDDLGLGGNELSKTTGNAGGRIACGVIGLAKI


Target MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGLAKGLHGFHVHEFGDNTNGCMSSGPHFNPYGKEHGAPVDENRHL
3l9y.1.B MPAKAVCVLRGDVSGTVFFDQQDEKSPVVVSGEVQGLTKGKHGFHVHEFGDNTNGCTSAGAHFNPEKQDHGGPSSAVRHV

Target GDLGNIEATGD-CPTKVNITDSKITLFGADSIIGRTVVVHADADDLGQGGHELSKSTGNAGARIGCGVIGIAKV
3l9y.1.B GDLGNIEAIEDAGVTKVSIQDSQISLHGPNSIIGRTLVVHADPDDLGLGGNELSKTTGNAGGRIACGVIGLAKI




Materials and Methods

Template Search

Template search with has been performed against the SWISS-MODEL template library (SMTL, last update: 2023-12-24, last included PDB release: 2023-12-15).

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

Table T1:

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

MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGLAKGLHGFHVHEFGDNTNGCMSSGPHFNPYGKEHGAPVDENRHLGDLGNIEATGDCPTKVNITD
SKITLFGADSIIGRTVVVHADADDLGQGGHELSKSTGNAGARIGCGVIGIAKV

Table T2:

Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Coverage Description
3l9e.1.A 67.97 homo-dimer 0.92 HHblits X-ray 2.05Å 0.51 1.00 Superoxide dismutase [Cu-Zn]
3l9y.1.A 67.97 homo-dimer 0.92 HHblits X-ray 1.80Å 0.51 1.00 Superoxide dismutase [Cu-Zn]
3l9e.1.A 68.63 homo-dimer 0.92 BLAST X-ray 2.05Å 0.51 1.00 Superoxide dismutase [Cu-Zn]
3l9y.1.A 67.97 homo-dimer 0.89 BLAST X-ray 1.80Å 0.51 1.00 Superoxide dismutase [Cu-Zn]
P61852.1.A 100.00 monomer - AFDB search AlphaFold v2 NA 0.62 1.00 Superoxide dismutase [Cu-Zn]
3gtv.1.A 60.67 homo-dimer 0.99 HHblits X-ray 2.20Å 0.48 0.98 Superoxide dismutase [Cu-Zn]
3gtv.1.A 61.33 homo-dimer 0.98 BLAST X-ray 2.20Å 0.49 0.98 Superoxide dismutase [Cu-Zn]
7wx0.1.A 60.00 homo-dimer 0.97 HHblits X-ray 1.40Å 0.48 0.98 Superoxide dismutase [Cu-Zn]
7wx0.1.A 60.93 homo-dimer 0.97 BLAST X-ray 1.40Å 0.48 0.99 Superoxide dismutase [Cu-Zn]
3gtt.1.A 59.60 homo-dimer 0.95 HHblits X-ray 2.40Å 0.49 0.99 Superoxide dismutase [Cu-Zn]
2zky.1.A 61.84 homo-dimer 0.94 BLAST X-ray 2.40Å 0.49 0.99 Superoxide dismutase [Cu-Zn]
3gtt.1.A 60.67 homo-dimer 0.94 BLAST X-ray 2.40Å 0.49 0.98 Superoxide dismutase [Cu-Zn]
1sda.1.B 58.39 homo-dimer 0.96 HHblits X-ray 2.50Å 0.48 0.97 COPPER,ZINC SUPEROXIDE DISMUTASE
1sda.1.A 58.39 homo-dimer 0.96 HHblits X-ray 2.50Å 0.48 0.97 COPPER,ZINC SUPEROXIDE DISMUTASE
7wx1.1.A 60.67 homo-dimer 0.94 HHblits X-ray 1.65Å 0.48 0.98 Superoxide dismutase [Cu-Zn]
4b3e.2.A 61.84 homo-dimer 0.93 BLAST X-ray 2.15Å 0.49 0.99 SUPEROXIDE DISMUTASE [CU-ZN]
7wx1.1.A 60.93 homo-dimer 0.93 BLAST X-ray 1.65Å 0.48 0.99 Superoxide dismutase [Cu-Zn]
1xso.1.A 61.49 homo-dimer 0.94 HHblits X-ray 1.49Å 0.49 0.97 COPPER,ZINC SUPEROXIDE DISMUTASE
3ltv.1.A 60.26 homo-dimer 0.92 HHblits X-ray 2.45Å 0.49 0.99 Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
7wwy.1.A 60.00 homo-dimer 0.92 HHblits X-ray 1.50Å 0.48 0.98 Superoxide dismutase [Cu-Zn]
7wwy.1.A 60.26 homo-dimer 0.92 BLAST X-ray 1.50Å 0.48 0.99 Superoxide dismutase [Cu-Zn]
2sod.2.A 58.39 homo-dimer 0.96 HHblits X-ray 2.00Å 0.48 0.97 COPPER,ZINC SUPEROXIDE DISMUTASE
1xso.1.A 62.59 homo-dimer 0.94 BLAST X-ray 1.49Å 0.49 0.96 COPPER,ZINC SUPEROXIDE DISMUTASE
7wwt.1.A 60.26 homo-dimer 0.91 HHblits X-ray 1.60Å 0.48 0.99 Superoxide dismutase [Cu-Zn]
8gsq.5.A 61.84 homo-dimer 0.91 BLAST X-ray 2.10Å 0.49 0.99 Superoxide dismutase [Cu-Zn]
3f7k.1.A 62.16 homo-dimer 0.92 HHblits X-ray 1.35Å 0.50 0.97 Copper,Zinc Superoxide Dismutase
7wwt.1.A 60.26 homo-dimer 0.91 BLAST X-ray 1.60Å 0.48 0.99 Superoxide dismutase [Cu-Zn]
7fb9.1.B 61.84 homo-dimer 0.90 BLAST X-ray 2.70Å 0.49 0.99 Superoxide dismutase [Cu-Zn]
7fb9.1.A 61.84 homo-dimer 0.90 BLAST X-ray 2.70Å 0.49 0.99 Superoxide dismutase [Cu-Zn]
3ltv.1.A 61.33 homo-dimer 0.89 BLAST X-ray 2.45Å 0.50 0.98 Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
2sod.1.A 58.39 homo-dimer 0.94 HHblits X-ray 2.00Å 0.48 0.97 COPPER,ZINC SUPEROXIDE DISMUTASE
1to4.1.A 59.33 homo-dimer 0.89 HHblits X-ray 1.55Å 0.48 0.98 Superoxide dismutase
2sod.1.B 58.39 homo-dimer 0.94 HHblits X-ray 2.00Å 0.48 0.97 COPPER,ZINC SUPEROXIDE DISMUTASE
1to4.1.A 60.40 homo-dimer 0.88 BLAST X-ray 1.55Å 0.48 0.97 Superoxide dismutase
3mnd.1.A 59.46 homo-dimer 0.88 BLAST X-ray 2.20Å 0.48 0.97 Superoxide dismutase [Cu-Zn]
2q2l.1.A 61.07 homo-dimer 0.54 HHblits X-ray 2.37Å 0.49 0.97 Superoxide Dismutase
1srd.1.A 56.67 homo-tetramer 0.54 HHblits X-ray 2.00Å 0.47 0.98 COPPER,ZINC SUPEROXIDE DISMUTASE
2q2l.1.A 62.16 homo-dimer 0.53 BLAST X-ray 2.37Å 0.49 0.97 Superoxide Dismutase
1srd.1.A 57.72 homo-tetramer 0.53 BLAST X-ray 2.00Å 0.48 0.97 COPPER,ZINC SUPEROXIDE DISMUTASE
6zs1.1.A 57.62 homo-octamer 0.51 HHblits X-ray 1.56Å 0.47 0.99 Superoxide dismutase [Cu-Zn]
6zs1.1.A 59.60 homo-octamer 0.49 BLAST X-ray 1.56Å 0.48 0.99 Superoxide dismutase [Cu-Zn]
8gsq.2.A 61.84 monomer - BLAST X-ray 2.10Å 0.49 0.99 Superoxide dismutase [Cu-Zn]
1e9o.1.B 58.39 monomer - HHblits X-ray 1.85Å 0.48 0.97 SUPEROXIDE DISMUTASE
1e9o.1.A 57.72 monomer - HHblits X-ray 1.85Å 0.48 0.97 SUPEROXIDE DISMUTASE
1e9o.1.A 59.33 monomer - BLAST X-ray 1.85Å 0.48 0.98 SUPEROXIDE DISMUTASE
1e9o.1.B 60.00 monomer - BLAST X-ray 1.85Å 0.48 0.98 SUPEROXIDE DISMUTASE
3f7k.1.A 61.33 homo-dimer 0.91 BLAST X-ray 1.35Å 0.49 0.98 Copper,Zinc Superoxide Dismutase
6a9o.4.A 61.84 homo-dimer 0.85 BLAST X-ray 2.50Å 0.49 0.99 Superoxide dismutase [Cu-Zn]
1dsw.1.A 58.67 monomer - HHblits NMR NA 0.47 0.98 SUPEROXIDE DISMUTASE (CU-ZN)
7vzf.1.C 61.84 homo-trimer - BLAST EM NA 0.49 0.99 Superoxide dismutase [Cu-Zn]

The table above shows the top 50 filtered templates. A further 236 templates were found which were considered to be less suitable for modelling than the filtered list.
1azv.1.A, 1azv.1.B, 1b4l.1.A, 1b4t.1.A, 1ba9.1.A, 1bzo.1.A, 1cb4.1.A, 1cob.1.A, 1do5.1.A, 1dsw.1.A, 1e9p.1.A, 1e9p.1.B, 1e9q.1.A, 1e9q.1.B, 1ej8.1.A, 1eqw.1.A, 1eso.1.A, 1f18.1.A, 1f1a.1.A, 1f1d.1.A, 1f1g.1.A, 1fun.1.A, 1hl4.2.A, 1ib5.1.A, 1ibb.1.A, 1ibd.1.A, 1ibf.1.A, 1ibh.1.A, 1jk9.1.A, 1jk9.1.B, 1kmg.1.A, 1l3n.1.A, 1l3n.1.B, 1mfm.1.A, 1n18.1.A, 1n19.1.A, 1oaj.1.A, 1oal.1.A, 1oez.2.B, 1ozt.3.A, 1ozu.1.A, 1ozu.1.B, 1p1v.1.A, 1ptz.1.A, 1ptz.1.B, 1pu0.4.A, 1pu0.5.A, 1pzs.1.A, 1qup.1.A, 1qup.1.B, 1rk7.1.A, 1s4i.1.A, 1s4i.3.A, 1sda.1.A, 1sda.1.B, 1sos.1.A, 1spd.1.A, 1spd.1.B, 1u3n.1.A, 1uxl.2.A, 1uxm.4.A, 1xtl.1.A, 1xtm.1.A, 1yai.1.A, 1z9n.1.A, 1z9p.1.A, 2af2.1.A, 2af2.1.B, 2aps.1.A, 2aqn.1.A, 2aqp.1.A, 2aqq.1.A, 2aqr.1.A, 2aqs.1.A, 2aqt.1.A, 2c9u.1.B, 2e46.1.A, 2e47.1.A, 2e47.1.B, 2gbt.1.A, 2gbt.2.A, 2gbu.1.A, 2gbu.2.A, 2gbv.4.A, 2jlp.1.A, 2jlp.1.B, 2jlp.2.A, 2k4w.1.A, 2lu5.1.A, 2mp3.1.A, 2nam.1.A, 2nnx.1.A, 2nnx.1.B, 2r27.1.A, 2sod.1.A, 2sod.1.B, 2sod.2.A, 2sod.2.B, 2v0a.1.A, 2vr6.1.A, 2vr7.1.A, 2wko.1.A, 2wwn.1.A, 2wyt.1.A, 2wyt.1.B, 2xjk.1.A, 2xjl.1.A, 2zkw.1.A, 2zkx.1.A, 2zkx.1.B, 2zky.1.A, 3ce1.1.A, 3cqp.1.B, 3cqp.2.A, 3cqq.1.A, 3cqq.1.B, 3ecu.1.B, 3ecv.1.B, 3ecv.2.B, 3ecw.1.A, 3gqf.1.B, 3gzo.2.B, 3gzp.1.A, 3gzq.1.A, 3gzq.1.B, 3h2p.1.A, 3h2p.1.B, 3h2q.1.A, 3hff.1.A, 3hog.1.A, 3k91.1.B, 3kbe.1.A, 3kbf.1.A, 3kh3.1.A, 3kh3.2.B, 3km2.3.B, 3km2.6.B, 3mnd.1.A, 3qqd.1.A, 3qqd.1.B, 3sod.1.A, 3t5w.6.B, 4a7g.1.A, 4a7u.1.A, 4a7v.1.A, 4b3e.2.A, 4bcy.1.A, 4bcz.1.A, 4bcz.2.A, 4bd4.1.A, 4bd4.4.A, 4bd4.5.A, 4bd4.9.A, 4ff9.1.B, 4l05.1.A, 4mcm.1.A, 4mcn.1.A, 4n3u.1.A, 4oh2.1.A, 4oh2.2.A, 4oh2.2.B, 4oh2.3.A, 4oh2.4.A, 4oh2.5.A, 4oja.1.A, 4rvp.1.A, 4u4i.1.A, 4u4i.1.B, 4xcr.1.A, 4xcr.2.A, 5in2.1.A, 5j07.1.A, 5j07.2.A, 5j0c.1.A, 5j0f.1.A, 5j0f.2.A, 5j0g.1.A, 5j0g.2.A, 5k02.1.A, 5kbk.1.A, 5kbl.1.A, 5kbm.1.A, 5u9m.1.B, 5u9m.2.A, 5yto.1.A, 5ytu.4.B, 6a9o.4.A, 6adq.1.H, 6d52.1.A, 6d52.2.B, 6dtk.1.A, 6flh.1.A, 6fn8.1.A, 6foi.1.A, 6fol.1.A, 6fol.1.B, 6fon.1.A, 6fp6.1.B, 6spa.1.B, 6spi.1.A, 6spj.1.B, 6vbs.1.A, 6vbs.1.B, 6vbs.2.A, 6vbs.2.B, 6vbs.3.A, 6vbs.3.B, 6vbt.1.A, 6vbt.1.B, 6z4o.1.A, 7b4p.1.B, 7b4p.2.A, 7cjv.1.A, 7cjw.1.A, 7fb6.1.A, 7fb6.2.A, 7fb9.1.A, 7fb9.1.B, 7fb9.7.A, 7fb9.8.A, 7nxx.1.A, 7rh5.1.E, 7rh5.1.F, 7t8e.1.A, 7t8f.1.B, 7vzf.1.C, 7ypp.1.A, 7ypp.2.A, 7ypp.2.B, 7ypr.1.A, 7ypr.1.B, 8gsq.2.A, 8gsq.3.A, 8gsq.4.A, 8gsq.4.B, 8gsq.5.A