|  | SWISS-MODEL Homology Modelling Report

## Model Building Report

This document lists the results for the homology modelling project "4_1_Jan_SF_Bin61_scaffold_1987_c1:3-2501_1" submitted to SWISS-MODEL workspace on March 29, 2023, 6:30 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 249 templates were found (Table T2).

## Models

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

### Model #02 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.70 | 0.68 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 37.28 | monomer | 0.00 | HHblits | X-ray | 2.97Å | 0.39 | 1 - 829 | 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    MPTANKADEVIILRPGTDAAFFLGVARELIEKGLYDRAAVIERTDLPLLVRLDTGERLDARDVIPGYELAALTNYVTLKP
    7b04.1.B  SPSAQKADYWIPIRNNTDTALFLGITKILIDNKWYDADYVKKFTDFPLLIRTDTLKRVSPKDIIPNYKLQDI--------

    Target    DAEIKGNPPPPPFTAGGQVVPTELRDAWGDFVWWDRATGRPRPVSRDEV---GARFDGDPALLGEFEVELVDGSTVPVRP
    7b04.1.B  --S---DG-PSYHIQG---LKDEQREIIGDFVVWDAKSKGPKAITRDDVGETLVKKGIDPVLEGSFKLKTIDGKEIEVMT

    Target    AFDLLKQYLDESFDLRTASEVCRVPPQAIQSIARQLAANKRETLLAAGMGPNHYFQNDLFGRVQFLVAALTDNIGHLGGN
    7b04.1.B  LLEMYKIHLR-DYDIDSVVSMTNSPKDLIERLAKDIATIKPVAI-HYGEGVNHYFHATLMNRSYYLPVMLTGNVGYFGSG

    Target    VGSYAGNYRGSVFQA---MG-QWIAEDPFA-IEPDLTKPAT------VKRYYKAESAHYWNYGERPLRAVAKDDEGDLTK
    7b04.1.B  SHTWAGNYKAGNFQASKWSGPGFYGWVAEDVFKPNL-DPYASAKDLNIKGRALDEEVAYWNHSERPLI-VNT---P-KYG

    Target    GEVLTGKSHMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPRQDAVFCNEWHWTSSCEYADLVFPADSWAEFKLPDATAS
    7b04.1.B  RKVFTGKTHMPSPTKVLWFTNVNLINNAKHV-YQMLKNVNPNIEQIMSTDIEITGSIEYADFAFPANSWVEFQEFEITNS

    Target    CTNPFLLAFPTTPLKRLYDTRSDYEALALTAKALGELIDEPRMEQYWRGILDGDPTPYLQRIFSGSNATRGITYDELHES
    7b04.1.B  CSNPFIQIWGKTGITPVYESKDDVKILAGMASKLGELLRDKRFEDNWKFAIEGRASVYINRLLDGSTTMKGYTCEDILNG

    Target    SKR--GVPLLMNMRTYPRSGGWEQRQEDKPWYTATGRLEFYRPEPEFQAAGESLPVWREPVDATFYEPNAILSNAAHPSI
    7b04.1.B  KYGEPGVAM-LLFRTYPRHPFWEQVHESLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGPEATPYLPNAIVST--NPYI

    Target    APRAPEDYGVPESQLDVETRQYRNVVRTWAELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVDADWISMLFGPFGDPY
    7b04.1.B  ---RPDDYGIPENAEYWEDRTVRNIKKSWEETKKTKNFL--WEKGYHFYCVTPKSRHTVHSQWAVTDWNFIWNNNFGDPY

    Target    RRDPRMPWTGEAYLEINPKDAAELGLADGDYAWVDADPEDRPYRGWKEDDPYYEVARAMMRVRIYTGMSRGVIRTWFNMY
    7b04.1.B  RMDKRMPGVGEHQIHIHPQAARDLGIEDGDYVYVDANPADRPYEGWKPNDSFYKVSRLMLRAKYNPAYPYNCTMMKHSAW

    Target    AATPATVANQKATPGNPARNEQTRYVALFRYGSHQSGTRAWLRPTQQTDSLVRKGYFGQVIGTGFEADVHSVSGAPKEAF
    7b04.1.B  ISSDKTVQAHETRPDGRALSP-SGYQSSFRYGSQQSITRDWSMPMHQLDSLFHKAKIGMKFIFGFEADNHCINTVPKETL

    Target    VKIEKAEDGGIGAERLWRPLTLGLRPEAPSAALTAYLAGDYSGTKGS
    7b04.1.B  VKITKAENGGMGGKGVWDPVKTGYTAGNENDFMKKFLNGELIKVD--

### Model #01 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.69 | 0.67 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 39.26 | monomer | 0.00 | BLAST | X-ray | 2.97Å | 0.40 | 2 - 824 | 0.95 | 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    MPTANKADEVIILRPGTDAAFFLGVARELIEKGLYDRAAVIERTDLPLLVRLDTGERLDARDVIPGYELAALTNYVTLKP
    7b04.1.B  -PSAQKADYWIPIRNNTDTALFLGITKILIDNKWYDADYVKKFTDFPLLIRTDTLKRVSPKDIIPNYKLQDISD----GP

    Target    DAEIKGNPPPPPFTAGGQVVPTELRDAWGDFVWWDRATGRPRPVSRDEVG---ARFDGDPALLGEFEVELVDGSTVPVRP
    7b04.1.B  SYHIQG-------------LKDEQREIIGDFVVWDAKSKGPKAITRDDVGETLVKKGIDPVLEGSFKLKTIDGKEIEVMT

    Target    AFDLLKQYLDESFDLRTASEVCRVPPQAIQSIARQLAANKRETLLAAGMGPNHYFQNDLFGRVQFLVAALTDNIGHLGGN
    7b04.1.B  LLEMYKIHLRD-YDIDSVVSMTNSPKDLIERLAKDIATIK-PVAIHYGEGVNHYFHATLMNRSYYLPVMLTGNVGYFGSG

    Target    VGSYAGNYRGSVFQA-------MGQWIAEDPFAIEPDL-----TKPATVKRYYKAESAHYWNYGERPLRAVAKDDEGDLT
    7b04.1.B  SHTWAGNYKAGNFQASKWSGPGFYGWVAEDVF--KPNLDPYASAKDLNIKGRALDEEVAYWNHSERPL-IVNTPKYGR--

    Target    KGEVLTGKSHMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPRQDAVFCNEWHWTSSCEYADLVFPADSWAEFKLPDATA
    7b04.1.B  --KVFTGKTHMPSPTKVLWFTNVN-LINNAKHVYQMLKNVNPNIEQIMSTDIEITGSIEYADFAFPANSWVEFQEFEITN

    Target    SCTNPFLLAFPTTPLKRLYDTRSDYEALALTAKALGELIDEPRMEQYWRGILDGDPTPYLQRIFSGSNATRGITYDELHE
    7b04.1.B  SCSNPFIQIWGKTGITPVYESKDDVKILAGMASKLGELLRDKRFEDNWKFAIEGRASVYINRLLDGSTTMKGYTCEDILN

    Target    SS--KRGVPLLMNMRTYPRSGGWEQRQEDKPWYTATGRLEFYRPEPEFQAAGESLPVWREPVDATFYEPNAILSNAAHPS
    7b04.1.B  GKYGEPGVAMLL-FRTYPRHPFWEQVHESLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGPEATPYLPNAIVS--TNPY

    Target    IAPRAPEDYGVPESQLDVETRQYRNVVRTWAELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVDADWISMLFGPFGDP
    7b04.1.B  IRP---DDYGIPENAEYWEDRTVRNIKKSWEETKKTKNFLWEK--GYHFYCVTPKSRHTVHSQWAVTDWNFIWNNNFGDP

    Target    YRRDPRMPWTGEAYLEINPKDAAELGLADGDYAWVDADPEDRPYRGWKEDDPYYEVARAMMRVRIYTGMSRGVIRTWFNM
    7b04.1.B  YRMDKRMPGVGEHQIHIHPQAARDLGIEDGDYVYVDANPADRPYEGWKPNDSFYKVSRLMLRAKYNPAYPYNCTMMKHSA

    Target    YAATPATVANQKATPGNPARNEQTRYVALFRYGSHQSGTRAWLRPTQQTDSLVRKGYFGQVIGTGFEADVHSVSGAPKEA
    7b04.1.B  WISSDKTVQAHETRPDGRALSP-SGYQSSFRYGSQQSITRDWSMPMHQLDSLFHKAKIGMKFIFGFEADNHCINTVPKET

    Target    FVKIEKAEDGGIGAERLWRPLTLGLRPEAPSAALTAYLAGDYSGTKGS
    7b04.1.B  LVKITKAENGGMGGKGVWDPVKTGYTAGNENDFMKKFLNGE-------

### Model #03 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.38 | 0.43 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
3ir5.1.A | 23.01 | monomer | 0.00 | HHblits | X-ray | 2.30Å | 0.31 | 1 - 795 | 0.78 | Respiratory nitrate reductase 1 alpha chain

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
6MO.3 | Binding site not conserved. | MOLYBDENUM(VI) ION
AGA.5 | Binding site not conserved. | (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
F3S.9 | Binding site not conserved. | FE3-S4 CLUSTER
HEM.10 | Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
HEM.11 | Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
MD1.1 | 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
MD1.2 | 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
SF4.4 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.6 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.7 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.8 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    MPTANKADEVIILRPGTDAAFFLGVARELIEKGL------YDRAAVIERTDLPLLVRLD-------TGERLDARDVIPGY
    3ir5.1.A  AEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYTDMPMLVMLEERDGYYAAGRMLRAADLVDAL

    Target    ELAALTNYVTLKPDAEIKGNPPPPPFTAGGQVVPTELRDAWGDFVWWDRATGRPRPVSRDEV------------------
    3ir5.1.A  GQ---------EN-------------------------NPEWKTVAFNT-NGEMVAPNGSIGFRWGEKGKWNLEQRDGKT

    Target    ---------------------GARF-----------DGDPALLG---EFEVELVDGSTVPVRPAFDLLK-----------
    3ir5.1.A  GEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVYDLTLANYGLERGLND

    Target    -------QYLDESFDLRTASEVCRVPPQAIQSIARQLAAN-----KRETLLAAGMGPNHYFQNDLFGRVQFLVAALTDNI
    3ir5.1.A  VNCATSYDDVK-AYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRS-MIIVGAGLNHWYHLDMNYRGLINMLIFCGCV

    Target    GHLGGNVGSYAGNYRGSVFQAMGQWIAEDPFAI-----------E--------P-----DLTKPA-TVKRYYKA------
    3ir5.1.A  GQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEELLSPMADKSRYTGHLIDFNV

    Target    --ESAHYW----NYGERPLRAVAKD-----DEGDLTKGEVLTGKS--------HMPTPTKLIWFGNSNSLLGNAKWSFDV
    3ir5.1.A  RAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLFIWRSNLLGSSGKGHEFM

    Target    V------------------------------KNTLPRQDAVFCNEWHWTSSCEYADLVFPADSWAEFKLPDATASCTNPF
    3ir5.1.A  LKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYEK--DDMNTSDMHPF

    Target    LLAFPTTPLKRLYDTRSDYEALALTAKALGELIDE---------------PR---------MEQYWRGILDG--------
    3ir5.1.A  IHP-LSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPIQHDSAAELAQPLDVKDWKKGECDLIPGKTAPH

    Target    ------D-------------------------------PTPYLQRI-------------------------FSGSNATRG
    3ir5.1.A  IMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAIDAAEMILTLAPETNG

    Target    I----TYDELHESSK-----------RGVPLLMNMR------------------TYPRSGGWEQRQEDKPWYTATGRLEF
    3ir5.1.A  QVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYTNVHELIPWRTLSGRQQL

    Target    YRPEPEFQAAGESLPVWREPVDATFYEPNAILSNAAHPSIAPRAPEDYGVPESQLDVETRQYRNVVRTWAELQQTLHPLQ
    3ir5.1.A  YQDHQWMRDFGESLLVYRPPIDTRSV------------------KEVI----------------------G------QKS

    Target    ERDPAFRFVFQTPKYRWGAHSTAVDADWISMLFGPFGDPYRRDPRMPWTGEAYLEINPKDAAELGLADGDYAWVDADPED
    3ir5.1.A  NGNQEKALNFLTPHQKWGIHSTYSDNLLMLTLG---------------RGGPVVWLSEADAKDLGIADNDWIEVFNS---

    Target    RPYRGWKEDDPYYEVARAMMRVRIYTGMSRGVIRTWFNMYAATPATVANQKATPGNPARNEQTRYVALFRYGSHQSGTRA
    3ir5.1.A  --------------NGALTARAVVSQRVPAGMTMMYHAQERIVN--------LPGSEIT--------QQRGGIHNSVTRI

    Target    WLRPTQQTDSLVRKGYFGQVIGTGFEADVHSVSGAPKEAFVKIEKAEDGGIGAERLWRPLTLGLRPEAPSAALTAYLAGD
    3ir5.1.A  TPKPTHMI------GGYAHL-AYGFN--YYGTVGSNRDEFVVVRKMKNIDW-----------------------------

    Target    YSGTKGS
    3ir5.1.A  -------

### Model #04 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.12 | 0.35 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
2fug.2.C | 20.00 | monomer | 0.00 | HHblits | X-ray | 3.30Å | 0.28 | 342 - 706 | 0.23 | NADH-quinone oxidoreductase chain 3

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
FES.2 | Binding site not conserved. | FE2/S2 (INORGANIC) CLUSTER
FES.6 | Binding site not conserved. | FE2/S2 (INORGANIC) CLUSTER
FMN.10 | Binding site not conserved. | FLAVIN MONONUCLEOTIDE
SF4.1 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.3 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.4 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.5 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.7 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.8 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.9 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    MPTANKADEVIILRPGTDAAFFLGVARELIEKGLYDRAAVIERTDLPLLVRLDTGERLDARDVIPGYELAALTNYVTLKP
    2fug.2.C  --------------------------------------------------------------------------------

    Target    DAEIKGNPPPPPFTAGGQVVPTELRDAWGDFVWWDRATGRPRPVSRDEVGARFDGDPALLGEFEVELVDGSTVPVRPAFD
    2fug.2.C  --------------------------------------------------------------------------------

    Target    LLKQYLDESFDLRTASEVCRVPPQAIQSIARQLAANKRETLLAAGMGPNHYFQNDLFGRVQFLVAALTDNIGHLGGNVGS
    2fug.2.C  --------------------------------------------------------------------------------

    Target    YAGNYRGSVFQAMGQWIAEDPFAIEPDLTKPATVKRYYKAESAHYWNYGERPLRAVAKDDEGDLTKGEVLTGKSHMPTPT
    2fug.2.C  --------------------------------------------------------------------------------

    Target    KLIWFGNSNSLLGNAKWSFDVVKNTLPRQDAVFCNEWHWTSSC-EYADLVFPADSWAEFKLPDATASCTNPFLLAFPTTP
    2fug.2.C  ---------------------PEEALKGKRFVVMHLSHLHPLAERYAHVVLPAPTFYEKRG---HLVNLEGRVLPL-SPA

    Target    LKRLYDTRSDYEALALTAKALGELIDEPRMEQYWRGILDGDPTPYLQRIFSGSNATRGITYDELHESSKRGVPLLMNMRT
    2fug.2.C  PIENGEAEGALQVLALLAEALGVRPPFRL------------HLEA---------------QKALK---------------

    Target    YPRSGGWEQRQEDKPWYTATGRLEFYRPEPEFQAAGESLPVWREPVDATFYEPNAILSNAAHPSIAPRAPEDYGVPESQL
    2fug.2.C  ------------ARKVPEAMGRLSFRLKELR-------------P-----------------------------------

    Target    DVETRQYRNVVRTWAELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVDADWISMLFGPFGDPYRRDPRMPWTGEAYLE
    2fug.2.C  --------------------------KERKGAFYLRPTMWKAHQ-----AVGKAQEA-----------------ARAELW

    Target    INPKDAAELGLADGDYAWVDADPEDRPYRGWKEDDPYYEVARAMMRVRIYTGMSRGVIRTWFNMYAATPATVANQKATPG
    2fug.2.C  AHPETARAEALPEGAQVAVETP-----------------FGRVEARVVHREDVPKGHLYLSALGPAAG------------

    Target    NPARNEQTRYVALFRYGSHQSGTRAWLRPTQQTDSLVRKGYFGQVIGTGFEADVHSVSGAPKEAFVKIEKAEDGGIGAER
    2fug.2.C  --------------------------------------------------------------------------------

    Target    LWRPLTLGLRPEAPSAALTAYLAGDYSGTKGS
    2fug.2.C  --------------------------------

## 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.

MPTANKADEVIILRPGTDAAFFLGVARELIEKGLYDRAAVIERTDLPLLVRLDTGERLDARDVIPGYELAALTNYVTLKPDAEIKGNPPPPPFTAGGQVV
PTELRDAWGDFVWWDRATGRPRPVSRDEVGARFDGDPALLGEFEVELVDGSTVPVRPAFDLLKQYLDESFDLRTASEVCRVPPQAIQSIARQLAANKRET
LLAAGMGPNHYFQNDLFGRVQFLVAALTDNIGHLGGNVGSYAGNYRGSVFQAMGQWIAEDPFAIEPDLTKPATVKRYYKAESAHYWNYGERPLRAVAKDD
EGDLTKGEVLTGKSHMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPRQDAVFCNEWHWTSSCEYADLVFPADSWAEFKLPDATASCTNPFLLAFPTTPL
KRLYDTRSDYEALALTAKALGELIDEPRMEQYWRGILDGDPTPYLQRIFSGSNATRGITYDELHESSKRGVPLLMNMRTYPRSGGWEQRQEDKPWYTATG
RLEFYRPEPEFQAAGESLPVWREPVDATFYEPNAILSNAAHPSIAPRAPEDYGVPESQLDVETRQYRNVVRTWAELQQTLHPLQERDPAFRFVFQTPKYR
WGAHSTAVDADWISMLFGPFGDPYRRDPRMPWTGEAYLEINPKDAAELGLADGDYAWVDADPEDRPYRGWKEDDPYYEVARAMMRVRIYTGMSRGVIRTW
FNMYAATPATVANQKATPGNPARNEQTRYVALFRYGSHQSGTRAWLRPTQQTDSLVRKGYFGQVIGTGFEADVHSVSGAPKEAFVKIEKAEDGGIGAERL
WRPLTLGLRPEAPSAALTAYLAGDYSGTKGS

## Table T2:

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 39.26 | monomer | - | BLAST | X-ray | 2.97Å | 0.40 | 0.95 | Nitrite oxidoreductase subunit A
7b04.1.B | 37.28 | monomer | - | HHblits | X-ray | 2.97Å | 0.39 | 0.96 | Nitrite oxidoreductase subunit A
7b04.2.B | 39.26 | monomer | - | BLAST | X-ray | 2.97Å | 0.40 | 0.95 | Nitrite oxidoreductase subunit A
7b04.2.B | 37.28 | monomer | - | HHblits | X-ray | 2.97Å | 0.39 | 0.96 | Nitrite oxidoreductase subunit A
5e7o.1.A | 26.27 | monomer | - | HHblits | X-ray | 2.40Å | 0.33 | 0.73 | DMSO reductase family type II enzyme, molybdopterin subunit
4ydd.1.A | 26.07 | monomer | - | HHblits | X-ray | 1.86Å | 0.33 | 0.73 | DMSO reductase family type II enzyme, molybdopterin subunit
2ivf.1.A | 26.18 | monomer | - | HHblits | X-ray | 1.88Å | 0.32 | 0.74 | ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
3ir5.1.A | 23.01 | monomer | - | HHblits | X-ray | 2.30Å | 0.31 | 0.78 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 23.62 | monomer | - | HHblits | X-ray | 2.50Å | 0.31 | 0.78 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 23.27 | homo-dimer | 0.06 | HHblits | X-ray | 1.90Å | 0.32 | 0.78 | Respiratory nitrate reductase 1 alpha chain
1r27.4.A | 23.16 | homo-dimer | 0.05 | HHblits | X-ray | 2.00Å | 0.31 | 0.78 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 23.38 | monomer | - | HHblits | X-ray | 1.90Å | 0.31 | 0.78 | Respiratory nitrate reductase 1 alpha chain
3ir6.1.A | 23.46 | monomer | - | HHblits | X-ray | 2.80Å | 0.32 | 0.78 | Respiratory nitrate reductase 1 alpha chain
1aa6.1.A | 19.87 | monomer | - | HHblits | X-ray | 2.30Å | 0.31 | 0.54 | FORMATE DEHYDROGENASE H
2iv2.1.A | 19.87 | monomer | - | HHblits | X-ray | 2.27Å | 0.31 | 0.54 | Formate dehydrogenase H
1fdo.1.A | 19.87 | monomer | - | HHblits | X-ray | 2.80Å | 0.31 | 0.54 | FORMATE DEHYDROGENASE H
1dms.1.A | 19.83 | monomer | - | HHblits | X-ray | 1.88Å | 0.30 | 0.58 | DMSO REDUCTASE
1e5v.2.A | 20.29 | monomer | - | HHblits | X-ray | 2.40Å | 0.30 | 0.58 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
7l5i.1.A | 19.58 | monomer | - | HHblits | X-ray | 1.73Å | 0.30 | 0.58 | Trimethylamine-N-oxide reductase
1e60.1.A | 20.21 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.58 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
7l5s.1.A | 19.58 | monomer | - | HHblits | X-ray | 2.09Å | 0.30 | 0.58 | Trimethylamine-N-oxide reductase
4dmr.1.A | 20.08 | monomer | - | HHblits | X-ray | 1.90Å | 0.30 | 0.58 | DMSO REDUCTASE
7z0t.1.G | 19.87 | monomer | - | HHblits | EM | NA | 0.31 | 0.54 | Formate dehydrogenase H
1eu1.1.A | 20.81 | monomer | - | HHblits | X-ray | 1.30Å | 0.31 | 0.57 | DIMETHYL SULFOXIDE REDUCTASE
1e18.1.A | 20.08 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.58 | DMSO REDUCTASE.
4ydd.1.A | 31.43 | monomer | - | BLAST | X-ray | 1.86Å | 0.36 | 0.57 | DMSO reductase family type II enzyme, molybdopterin subunit
5e7o.1.A | 31.43 | monomer | - | BLAST | X-ray | 2.40Å | 0.36 | 0.57 | DMSO reductase family type II enzyme, molybdopterin subunit
6tg9.1.A | 20.05 | monomer | - | HHblits | EM | 3.24Å | 0.30 | 0.53 | Formate dehydrogenase subunit alpha
2ivf.1.A | 40.10 | monomer | - | BLAST | X-ray | 1.88Å | 0.39 | 0.24 | ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
3m9s.1.C | 20.00 | monomer | - | HHblits | X-ray | 4.50Å | 0.28 | 0.23 | NADH-quinone oxidoreductase subunit 3
6zjl.1.C | 20.00 | monomer | - | HHblits | EM | NA | 0.28 | 0.23 | NADH-quinone oxidoreductase subunit 3
6ziy.1.C | 20.00 | monomer | - | HHblits | EM | NA | 0.28 | 0.23 | NADH-quinone oxidoreductase subunit 3
6zjn.1.C | 20.00 | monomer | - | HHblits | EM | NA | 0.28 | 0.23 | NADH-quinone oxidoreductase subunit 3
6q8o.1.C | 20.00 | monomer | - | HHblits | X-ray | 3.61Å | 0.28 | 0.23 | NADH-quinone oxidoreductase subunit 3
6zjy.1.C | 20.00 | monomer | - | HHblits | EM | NA | 0.28 | 0.23 | NADH-quinone oxidoreductase subunit 3
2fug.2.C | 20.00 | monomer | - | HHblits | X-ray | 3.30Å | 0.28 | 0.23 | NADH-quinone oxidoreductase chain 3
6zk9.1.C | 13.14 | monomer | - | HHblits | EM | NA | 0.27 | 0.21 | NADH:ubiquinone oxidoreductase core subunit S1
7zd6.1.4 | 13.14 | monomer | - | HHblits | EM | NA | 0.27 | 0.21 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6g72.1.G | 11.93 | monomer | - | HHblits | EM | NA | 0.26 | 0.21 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6zr2.1.G | 11.93 | monomer | - | HHblits | EM | 3.10Å | 0.26 | 0.21 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7ak6.1.G | 11.93 | monomer | - | HHblits | EM | NA | 0.26 | 0.21 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7ak5.1.G | 11.93 | monomer | - | HHblits | EM | NA | 0.26 | 0.21 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7dgr.10.A | 12.00 | monomer | - | HHblits | EM | NA | 0.26 | 0.21 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6qc5.1.C | 13.71 | monomer | - | HHblits | EM | NA | 0.27 | 0.21 | NADH:ubiquinone oxidoreductase core subunit S1
6qcf.1.C | 13.71 | monomer | - | HHblits | EM | NA | 0.27 | 0.21 | NADH:ubiquinone oxidoreductase core subunit S1
5o31.1.8 | 12.00 | monomer | - | HHblits | EM | 4.13Å | 0.26 | 0.21 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7zm7.1.I | 18.48 | monomer | - | HHblits | EM | NA | 0.30 | 0.11 | NADH-ubiquinone oxidoreductase-like protein
7v2c.1.L | 15.96 | monomer | - | HHblits | EM | NA | 0.29 | 0.11 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
5t5i.1.D | 17.50 | homo-dimer | - | HHblits | X-ray | 1.90Å | 0.31 | 0.10 | Tungsten formylmethanofuran dehydrogenase subunit fwdD
1h0h.1.A | 16.67 | monomer | - | HHblits | X-ray | 1.80Å | 0.30 | 0.09 | FORMATE DEHYDROGENASE SUBUNIT ALPHA

The table above shows the top 50 filtered templates. A further 175 templates were found which were considered to be less suitable for modelling than the filtered list.
1cz4.1.A, 1cz5.1.A, 1g8j.1.A, 1g8k.1.A, 1h0h.1.A, 1kqf.1.A, 1ogy.1.A, 1pt1.1.A, 1q16.1.A, 1r27.4.A, 1tmo.1.A, 1uhd.1.B, 1uhe.1.B, 1wlf.1.A, 1z0r.1.B, 2d9r.1.A, 2e7z.1.A, 2fy9.1.A, 2ivf.1.A, 2k1n.1.C, 2k1n.1.D, 2k1n.1.E, 2k1n.1.F, 2ki8.1.A, 2mrn.1.A, 2mru.1.A, 2mru.1.B, 2nya.1.A, 2pjh.1.B, 2ro3.1.A, 2ro4.1.A, 2v3v.1.A, 2v45.1.A, 2vpx.1.D, 2vpz.1.A, 2x48.1.A, 2x48.2.A, 2x48.3.A, 3egw.1.A, 3hu1.1.A, 3ir5.1.A, 3ir6.1.A, 3ir7.1.A, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3qc8.1.A, 3qq7.1.A, 3qq8.1.A, 3qwz.1.A, 3tiw.1.A, 3tiw.2.A, 4aay.1.A, 4ga5.1.A, 4ga6.1.A, 4kdi.1.A, 4kdi.2.A, 4kdl.1.A, 4nvs.1.A, 4rv0.1.A, 4v4c.1.A, 4ydd.1.A, 5b6c.1.A, 5cuo.1.A, 5cup.1.A, 5e7o.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, 5glf.1.A, 5glf.2.A, 5glf.3.A, 5glf.4.A, 5gpn.24.A, 5nqd.1.A, 5t5i.1.B, 5x4l.1.A, 5x4l.2.A, 5xtb.1.L, 6btm.1.B, 6cz7.1.A, 6f0k.1.B, 6gcs.1.A, 6hd3.1.A, 6lod.1.B, 6rfq.1.A, 6rfs.1.A, 6s6y.1.B, 6sdr.1.A, 6sdv.1.A, 6x89.1.H, 6yj4.1.G, 7a23.1.O, 7a8y.1.B, 7a8y.1.D, 7aqr.1.F, 7ar7.1.G, 7ar8.1.G, 7arc.1.F, 7b04.1.B, 7b04.2.B, 7bkb.1.F, 7bkb.1.J, 7bkb.1.L, 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, 7e5z.1.A, 7nz1.1.E, 7p61.1.C, 7p63.1.C, 7q5y.1.A, 7qsd.1.G, 7qv7.1.L, 7qv7.1.O, 7t2r.1.A, 7t30.1.A, 7tgh.58.A, 7vw6.1.A, 7vxu.1.L, 7wbb.1.A, 7wbb.1.B, 7wbb.1.C, 7wbb.1.D, 7wbb.1.E, 7wbb.1.G, 8b9z.1.G, 8ba0.1.G, 8bqg.1.A, 8e73.55.A, 8e9g.1.G