|  | SWISS-MODEL Homology Modelling Report

## Model Building Report

This document lists the results for the homology modelling project "4_1_May_SF_Bin52_scaffold_9609_c1_4099-4944_1" submitted to SWISS-MODEL workspace on March 29, 2023, 8:38 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:

- Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 (2018).
- Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319 (2017).
- Studer, G., Tauriello, G., Bienert, S., Biasini, M., Johner, N., Schwede, T. ProMod3 - A versatile homology modelling toolbox. PLOS Comp. Biol. 17(1), e1008667 (2021).
- Studer, G., Rempfer, C., Waterhouse, A.M., Gumienny, G., Haas, J., Schwede, T. QMEANDisCo - distance constraints applied on model quality estimation. Bioinformatics 36, 1765-1771 (2020).
- Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., Schwede, T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports 7 (2017).

## Results

The SWISS-MODEL template library (SMTL version 2023-03-23, PDB release 2023-03-17) 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 222 templates were found (Table T2).

## Models

The following models were built (see Materials and Methods "Model Building"):

### Model #01 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.70 | 0.67 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 38.29 | monomer | 0.00 | BLAST | X-ray | 2.97Å | 0.39 | 3 - 274 | 0.96 | Nitrite oxidoreductase subunit A

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
CA.10 | Binding site not conserved. | CALCIUM ION
CA.11 | Binding site not conserved. | CALCIUM ION
F3S.4 | Binding site not conserved. | FE3-S4 CLUSTER
HEM.9 | Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
MD1.5 | Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MD1.6 | Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MO.7 | Binding site not conserved. | MOLYBDENUM ATOM
SF4.1 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.2 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.3 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.8 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    GLGVPESQLDVETRQYRNVVRTWAELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVDADWISMLFGPFGDPYRRDPRM
    7b04.1.B  --GIPENAEYWEDRTVRNIKKSWEETKKTKNFLWEK--GYHFYCVTPKSRHTVHSQWAVTDWNFIWNNNFGDPYRMDKRM

    Target    PWTGEAYLEINPKDAAELGLADGDYAWVDADPEDRPYRGWNEDDPYYEVARAMMRVRIYTGMSRGVIRTWFNMYAATPAT
    7b04.1.B  PGVGEHQIHIHPQAARDLGIEDGDYVYVDANPADRPYEGWKPNDSFYKVSRLMLRAKYNPAYPYNCTMMKHSAWISSDKT

    Target    VANQKATPGNPARNEQTRYVALFRYGSHQSGTRAWLRPTQQTDSLVRKGYFGQVIGTGFEADVHSVSGAPKEAFVKIEKA
    7b04.1.B  VQAHETRPDGRALSP-SGYQSSFRYGSQQSITRDWSMPMHQLDSLFHKAKIGMKFIFGFEADNHCINTVPKETLVKITKA

    Target    EDGGIGAERLWRPLTLGLRPEAPSAALTAYLAGDYSGTKGS
    7b04.1.B  ENGGMGGKGVWDPVKTGYTAGNENDFMKKFLNGE-------

### Model #02 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.08 | 0.43 ± 0.11

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
3hu1.1.A | 17.91 | monomer | 0.00 | HHblits | X-ray | 2.81Å | 0.26 | 86 - 153 | 0.24 | Transitional endoplasmic reticulum ATPase

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
AGS.1 | Binding site not conserved. | PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
AGS.3 | Binding site not conserved. | PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
AGS.5 | Binding site not conserved. | PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
AGS.7 | Binding site not conserved. | PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
AGS.9 | Binding site not conserved. | PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
AGS.11 | Binding site not conserved. | PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
MG.2 | Not in contact with model. | MAGNESIUM ION
MG.4 | Not in contact with model. | MAGNESIUM ION
MG.6 | Not in contact with model. | MAGNESIUM ION
MG.8 | Not in contact with model. | MAGNESIUM ION
MG.10 | Not in contact with model. | MAGNESIUM ION
MG.12 | Not in contact with model. | MAGNESIUM ION

    Target    GLGVPESQLDVETRQYRNVVRTWAELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVDADWISMLFGPFGDPYRRDPRM
    3hu1.1.A  --------------------------------------------------------------------------------

    Target    PWTGEAYLEINPKDAAELGLADGDYAWVDADPEDRPYRGWN--EDDPYYEVARAMMRVRIYTGMSRGVIRTWFNMYAATP
    3hu1.1.A  -----SVVSLSQPKMDELQLFRGDTVLLKGKKR-REAVCIVLSDDTCSDEKIRMNRVVRNNLRVGLGDVISIQPC-----

    Target    ATVANQKATPGNPARNEQTRYVALFRYGSHQSGTRAWLRPTQQTDSLVRKGYFGQVIGTGFEADVHSVSGAPKEAFVKIE
    3hu1.1.A  --------------------------------------------------------------------------------

    Target    KAEDGGIGAERLWRPLTLGLRPEAPSAALTAYLAGDYSGTKGS
    3hu1.1.A  -------------------------------------------

## Materials and Methods

## Template Search

Template search with has been performed against the SWISS-MODEL template library (SMTL, last update: 2023-03-23, last included PDB release: 2023-03-17).

## 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 (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

- BLAST
  Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L. BLAST+: architecture and applications. BMC Bioinformatics 10, 421-430 (2009).
- HHblits
  Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J., Söding, J. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20, 473 (2019).

## Table T1:

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

GLGVPESQLDVETRQYRNVVRTWAELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVDADWISMLFGPFGDPYRRDPRMPWTGEAYLEINPKDAAELGL
ADGDYAWVDADPEDRPYRGWNEDDPYYEVARAMMRVRIYTGMSRGVIRTWFNMYAATPATVANQKATPGNPARNEQTRYVALFRYGSHQSGTRAWLRPTQ
QTDSLVRKGYFGQVIGTGFEADVHSVSGAPKEAFVKIEKAEDGGIGAERLWRPLTLGLRPEAPSAALTAYLAGDYSGTKGS

## Table T2:

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 38.29 | monomer | - | BLAST | X-ray | 2.97Å | 0.39 | 0.96 | Nitrite oxidoreductase subunit A
7b04.1.B | 37.45 | monomer | - | HHblits | X-ray | 2.97Å | 0.39 | 0.95 | Nitrite oxidoreductase subunit A
7b04.2.B | 38.29 | monomer | - | BLAST | X-ray | 2.97Å | 0.39 | 0.96 | Nitrite oxidoreductase subunit A
7b04.2.B | 37.45 | monomer | - | HHblits | X-ray | 2.97Å | 0.39 | 0.95 | Nitrite oxidoreductase subunit A
3ir5.1.A | 23.18 | monomer | - | HHblits | X-ray | 2.30Å | 0.32 | 0.54 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 23.18 | monomer | - | HHblits | X-ray | 1.90Å | 0.32 | 0.54 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 22.52 | monomer | - | HHblits | X-ray | 2.50Å | 0.32 | 0.54 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 23.65 | monomer | - | HHblits | X-ray | 1.90Å | 0.32 | 0.53 | Respiratory nitrate reductase 1 alpha chain
1r27.4.A | 23.18 | monomer | - | HHblits | X-ray | 2.00Å | 0.32 | 0.54 | Respiratory nitrate reductase 1 alpha chain
3ir6.1.A | 23.65 | monomer | - | HHblits | X-ray | 2.80Å | 0.32 | 0.53 | Respiratory nitrate reductase 1 alpha chain
4ydd.1.A | 27.14 | monomer | - | HHblits | X-ray | 1.86Å | 0.34 | 0.50 | DMSO reductase family type II enzyme, molybdopterin subunit
5e7o.1.A | 27.14 | monomer | - | HHblits | X-ray | 2.40Å | 0.34 | 0.50 | DMSO reductase family type II enzyme, molybdopterin subunit
2ivf.1.A | 25.00 | monomer | - | HHblits | X-ray | 1.88Å | 0.30 | 0.48 | ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
6cz7.1.A | 18.68 | monomer | - | HHblits | X-ray | 1.62Å | 0.31 | 0.32 | ArrA
7l5s.1.A | 16.47 | monomer | - | HHblits | X-ray | 2.09Å | 0.30 | 0.30 | Trimethylamine-N-oxide reductase
7l5i.1.A | 16.47 | monomer | - | HHblits | X-ray | 1.73Å | 0.30 | 0.30 | Trimethylamine-N-oxide reductase
7nz1.1.E | 20.48 | monomer | - | HHblits | EM | NA | 0.30 | 0.30 | NADH-quinone oxidoreductase subunit G
4dmr.1.A | 22.35 | monomer | - | HHblits | X-ray | 1.90Å | 0.30 | 0.30 | DMSO REDUCTASE
7p63.1.C | 20.48 | monomer | - | HHblits | EM | NA | 0.30 | 0.30 | NADH-quinone oxidoreductase
1eu1.1.A | 22.35 | monomer | - | HHblits | X-ray | 1.30Å | 0.31 | 0.30 | DIMETHYL SULFOXIDE REDUCTASE
7p61.1.C | 20.48 | monomer | - | HHblits | EM | NA | 0.30 | 0.30 | NADH-quinone oxidoreductase
1e60.1.A | 21.18 | monomer | - | HHblits | X-ray | 2.00Å | 0.29 | 0.30 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e18.1.A | 21.18 | monomer | - | HHblits | X-ray | 2.00Å | 0.29 | 0.30 | DMSO REDUCTASE.
1dms.1.A | 21.18 | monomer | - | HHblits | X-ray | 1.88Å | 0.29 | 0.30 | DMSO REDUCTASE
6tg9.1.A | 27.38 | monomer | - | HHblits | EM | 3.24Å | 0.33 | 0.30 | Formate dehydrogenase subunit alpha
1e5v.2.A | 21.18 | monomer | - | HHblits | X-ray | 2.40Å | 0.30 | 0.30 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
7vw6.1.A | 22.89 | monomer | - | HHblits | EM | NA | 0.30 | 0.30 | Formate dehydrogenase
4v4c.1.A | 14.44 | monomer | - | HHblits | X-ray | 2.35Å | 0.30 | 0.32 | Pyrogallol hydroxytransferase large subunit
2iv2.1.A | 20.24 | monomer | - | HHblits | X-ray | 2.27Å | 0.32 | 0.30 | Formate dehydrogenase H
1g8j.1.A | 21.69 | monomer | - | HHblits | X-ray | 2.03Å | 0.30 | 0.30 | ARSENITE OXIDASE
4aay.1.A | 18.82 | homo-dimer | - | HHblits | X-ray | 2.70Å | 0.30 | 0.30 | AROA
1fdo.1.A | 20.24 | monomer | - | HHblits | X-ray | 2.80Å | 0.32 | 0.30 | FORMATE DEHYDROGENASE H
5nqd.1.A | 18.82 | homo-dimer | - | HHblits | X-ray | 2.20Å | 0.30 | 0.30 | AroA
1aa6.1.A | 20.24 | monomer | - | HHblits | X-ray | 2.30Å | 0.32 | 0.30 | FORMATE DEHYDROGENASE H
1g8k.1.A | 21.69 | monomer | - | HHblits | X-ray | 1.64Å | 0.30 | 0.30 | ARSENITE OXIDASE
7z0t.1.G | 20.24 | monomer | - | HHblits | EM | NA | 0.32 | 0.30 | Formate dehydrogenase H
5t5i.1.D | 17.50 | homo-dimer | - | HHblits | X-ray | 1.90Å | 0.31 | 0.28 | Tungsten formylmethanofuran dehydrogenase subunit fwdD
1h0h.1.A | 15.58 | monomer | - | HHblits | X-ray | 1.80Å | 0.30 | 0.27 | FORMATE DEHYDROGENASE SUBUNIT ALPHA
3m9s.1.C | 21.43 | monomer | - | HHblits | X-ray | 4.50Å | 0.28 | 0.20 | NADH-quinone oxidoreductase subunit 3
6zjn.1.C | 21.43 | monomer | - | HHblits | EM | NA | 0.28 | 0.20 | NADH-quinone oxidoreductase subunit 3
6zjy.1.C | 21.43 | monomer | - | HHblits | EM | NA | 0.28 | 0.20 | NADH-quinone oxidoreductase subunit 3
6q8o.1.C | 21.43 | monomer | - | HHblits | X-ray | 3.61Å | 0.28 | 0.20 | NADH-quinone oxidoreductase subunit 3
3hu1.1.A | 17.91 | monomer | - | HHblits | X-ray | 2.81Å | 0.26 | 0.24 | Transitional endoplasmic reticulum ATPase
6zjl.1.C | 21.43 | monomer | - | HHblits | EM | NA | 0.28 | 0.20 | NADH-quinone oxidoreductase subunit 3
6ziy.1.C | 21.43 | monomer | - | HHblits | EM | NA | 0.28 | 0.20 | NADH-quinone oxidoreductase subunit 3
2vpz.1.A | 20.75 | monomer | - | HHblits | X-ray | 2.40Å | 0.30 | 0.19 | THIOSULFATE REDUCTASE
2vpx.1.D | 20.75 | monomer | - | HHblits | X-ray | 3.10Å | 0.30 | 0.19 | THIOSULFATE REDUCTASE
2fug.2.C | 21.43 | monomer | - | HHblits | X-ray | 3.30Å | 0.28 | 0.20 | NADH-quinone oxidoreductase chain 3
5cuo.1.A | 28.89 | monomer | - | HHblits | X-ray | 1.54Å | 0.35 | 0.16 | Phosphate propanoyltransferase
5cup.1.A | 28.89 | monomer | - | HHblits | X-ray | 2.10Å | 0.35 | 0.16 | Phosphate propanoyltransferase

The table above shows the top 50 filtered templates. A further 157 templates were found which were considered to be less suitable for modelling than the filtered list.
1cz4.1.A, 1cz5.1.A, 1kqf.1.A, 1ogy.1.A, 1tmo.1.A, 1wlf.1.A, 1yle.1.A, 2d9r.1.A, 2e7z.1.A, 2ki8.1.A, 2l66.1.A, 2nya.1.A, 2pjh.1.B, 2v3v.1.A, 2v45.1.A, 2w1t.1.A, 3idw.1.A, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3pjy.1.A, 3pjy.1.B, 3qc8.1.A, 3qq7.1.A, 3qq8.1.A, 3qwz.1.A, 3tiw.1.A, 3tiw.2.A, 4ga5.1.A, 4ga6.1.A, 4kdi.1.A, 4kdi.2.A, 4kdl.1.A, 4rv0.1.A, 5b6c.1.A, 5cuo.1.A, 5cup.1.A, 5e7p.1.A, 5epp.1.A, 5g4f.1.A, 5g4f.1.B, 5g4f.1.C, 5g4f.1.D, 5g4f.1.E, 5g4f.1.F, 5g4g.1.A, 5glf.1.A, 5glf.2.A, 5glf.3.A, 5glf.4.A, 5itm.1.A, 5itm.1.B, 5itm.1.E, 5naa.1.A, 5naa.2.A, 5udf.1.A, 5x4l.1.A, 5x4l.2.A, 6f0k.1.B, 6f3z.1.A, 6f3z.2.A, 6f49.1.A, 6hd3.1.A, 6lod.1.B, 6sdr.1.A, 6sdv.1.A, 6wkk.1.G, 6wkk.1.H, 6wkk.1.I, 6wkk.1.J, 6wkk.1.K, 6wkk.1.L, 6wkk.1.M, 6wkk.1.N, 6wkk.1.O, 6wkk.1.P, 6wkk.1.Q, 6wkk.1.R, 6wkk.1.S, 6wkk.1.T, 6wkk.1.U, 6wkk.1.V, 6wkk.1.W, 6wkk.1.X, 7arh.1.A, 7arh.1.B, 7ari.1.A, 7ari.1.B, 7arj.1.A, 7arj.1.B, 7ark.1.A, 7ark.1.B, 7arl.1.A, 7arl.1.B, 7arm.1.A, 7arm.1.B, 7bkb.1.J, 7dbo.1.A, 7dbo.2.A, 7dg7.1.A, 7dg9.1.A, 7di0.1.A, 7di0.2.A, 7di0.3.A, 7di1.1.A, 7du6.1.A, 7du7.1.A, 7dvc.1.A, 7dvc.5.A, 7dvf.1.A, 7dvh.1.A, 7dvh.2.A, 7dvh.4.A, 7dww.1.A, 7dww.2.A, 7dxr.1.A, 7dxr.1.B, 7dxr.2.B, 7dxs.1.A, 7dxs.1.B, 7dxs.2.A, 7dxs.2.B, 7dxt.1.A, 7dxu.1.A, 7dxu.1.B, 7dxu.2.B, 7dxv.1.A, 7dxv.1.B, 7dxw.1.A, 7dxx.1.A, 7dxx.1.B, 7dxy.1.A, 7dxz.1.A, 7dxz.2.A, 7dxz.2.B, 7dxz.3.A, 7dyc.1.A, 7dyc.2.A, 7dyc.3.A, 7mdx.1.A, 7mdx.1.B, 7mdy.1.A, 7mdy.1.B, 7v8i.1.A, 7v8i.1.C, 7v8l.1.A, 7v8l.1.C, 7v8m.1.A, 7v8m.1.C, 7wbb.1.A, 7wbb.1.B, 7wbb.1.C, 7wbb.1.D, 7wbb.1.E, 7wbb.1.G, 8bqg.1.A, 8e9g.1.G