|  | SWISS-MODEL Homology Modelling Report

## Model Building Report

This document lists the results for the homology modelling project "4_1_Oct_SF_Bin32_scaffold_7496_c1_2-2440_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 334 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 | 1 x MO: MOLYBDENUM ATOM; | 0.70 | 0.67 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 40.77 | monomer | 0.00 | BLAST | X-ray | 2.97Å | 0.41 | 1 - 811 | 0.95 | Nitrite oxidoreductase subunit A

### Included Ligands

Ligand | Description
--- | ---
1 x MO | MOLYBDENUM ATOM

### 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
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    SWDEATTIAAKTMEDVARTFNGDEGARKLLAQGYHPEMVEVMHGAGVQALKLRGGMPLLGIGRIFGFYRFANMLALLDRK
    7b04.1.B  SWDEAFTYASKGIIHITKKYSGPEGAQKLIDQGYPKEMVDRMQGAGTRTFKGRGGMGLLGVIGKYGMYRFNNCLAIVDAH

    Target    LRPDAPADEILGSRTFDNYAWHTDLPPGHPMVTGSQTVDFDLFSAEHTKLLLIIGMNWICTKMPDGHWIGDARLKGTRVI
    7b04.1.B  NRGVGP-DQALGGRNWSNYTWHGDQAPGHPFSHGLQTSDVDMNDVRFSKLLIQTGKNLIENKMPEAHWVTEVMERGGKIV

    Target    VISADYMPTANKADEVIILRPGTDAAFFLGVARELIEKGLYDRAAVIERTDLPLLVRLDTGERLDARDVIPGYELAALTN
    7b04.1.B  VITPEYSPSAQKADYWIPIRNNTDTALFLGITKILIDNKWYDADYVKKFTDFPLLIRTDTLKRVSPKDIIPNYKLQDISD

    Target    YVTLKPDAEIKGNPPPPPFTAGGQVVPTELRDAWGDFVWWDRATGRPRPVSRDEVG---ARFDGDPALLGEFEVELVDGS
    7b04.1.B  ----GPSYHIQG-------------LKDEQREIIGDFVVWDAKSKGPKAITRDDVGETLVKKGIDPVLEGSFKLKTIDGK

    Target    TVPVRPAFDLLKQYLDESFDLRTASEVCRVPPQAIQSIARQLAANKRETLLAAGMGPNHYFQNDLFGRVQFLVAALTDNI
    7b04.1.B  EIEVMTLLEMYKIHLRD-YDIDSVVSMTNSPKDLIERLAKDIATIK-PVAIHYGEGVNHYFHATLMNRSYYLPVMLTGNV

    Target    GHLGGNVGSYAGNYRGSVFQA-------MGQWIAEDPFAIEPDL-----TKPATVKRYYKAESAHYWNYGERPLRAVAKD
    7b04.1.B  GYFGSGSHTWAGNYKAGNFQASKWSGPGFYGWVAEDVF--KPNLDPYASAKDLNIKGRALDEEVAYWNHSERPL-IVNTP

    Target    DEGDLTKGEVLTGKSHMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPRQDAVFCNEWHWTSSCEYADLVFPADSWAEFK
    7b04.1.B  KYGR----KVFTGKTHMPSPTKVLWFTNVN-LINNAKHVYQMLKNVNPNIEQIMSTDIEITGSIEYADFAFPANSWVEFQ

    Target    LPDATASCTNPFLLAFPTTPLKRLYDTRSDYEALALTAKALGELIDEPRMEQYWRGILDGDPTPYLQRIFSGSNATRGIT
    7b04.1.B  EFEITNSCSNPFIQIWGKTGITPVYESKDDVKILAGMASKLGELLRDKRFEDNWKFAIEGRASVYINRLLDGSTTMKGYT

    Target    YDEL--HESSKRGVPLLMNMRTYPRSGGWEQRQEDKPWYTATGRLEFYRPEPEFQAAGESLPVWREPVDATFYEPNAILS
    7b04.1.B  CEDILNGKYGEPGVAMLL-FRTYPRHPFWEQVHESLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGPEATPYLPNAIVS

    Target    NAAHPSIAPRAPEDYGVPESQLDVETRQYRNVVRTWAELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVDADWISMLF
    7b04.1.B  --TNPYI---RPDDYGIPENAEYWEDRTVRNIKKSWEETKKTKNFLWEK--GYHFYCVTPKSRHTVHSQWAVTDWNFIWN

    Target    GPFGDPYRRDPRMPWTGEAYLEINPKDAA
    7b04.1.B  NNFGDPYRMDKRMPGVGEHQIHIHPQAA-

### Model #02 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.37 | 0.51 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
3ir5.1.A | 23.32 | monomer | 0.00 | HHblits | X-ray | 2.30Å | 0.32 | 1 - 588 | 0.62 | Respiratory nitrate reductase 1 alpha chain

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
6MO.3 | Not in contact with model. | 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    SWDEATTIAAKTMEDVARTFNGDEGARKLLAQGYHPEMVEVMHGAGVQALKLRGGMPLLGIGRIFGFYRFANMLALLDRK
    3ir5.1.A  SWQEVNELIAASNVYTIKN--------------YGPDRVAGFSPIPAMSMV-----------SYASGAR-----------

    Target    LRPDAPADEILGSRTFDNYAWHTDLPPGHPMVTGSQTVDFDLFSAEHTKLLLIIGMNWICTKMPDGHWIGDARLKGTRVI
    3ir5.1.A  ------YLSLIGGTCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGSNVPQTRTPDAHFFTEVRYKGTKTV

    Target    VISADYMPTANKADEVIILRPGTDAAFFLGVARELIEKGL------YDRAAVIERTDLPLLVRLD-------TGERLDAR
    3ir5.1.A  AVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYTDMPMLVMLEERDGYYAAGRMLRAA

    Target    DVIPGYELAALTNYVTLKPDAEIKGNPPPPPFTAGGQVVPTELRDAWGDFVWWDRATGRPRPVSRDEV------------
    3ir5.1.A  DLVDALGQE----------------------------------NNPEWKTVAFNT-NGEMVAPNGSIGFRWGEKGKWNLE

    Target    --------------------------G-ARFD-----------GDPALLG---EFEVELVDGSTVPVRPAFDLLK-----
    3ir5.1.A  QRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVYDLTLANYGL

    Target    -------------QYLDESFDLRTASEVCRVPPQAIQSIARQLAAN-----KRETLLAAGMGPNHYFQNDLFGRVQFLVA
    3ir5.1.A  ERGLNDVNCATSYDDVK-AYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRS-MIIVGAGLNHWYHLDMNYRGLINML

    Target    ALTDNIGHLGGNVGSYAGNYRGSVFQAMGQWIAEDPFAI-------------------EPD-----LTKPA-TVKRYYKA
    3ir5.1.A  IFCGCVGQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEELLSPMADKSRYTGH

    Target    --------ESAHYWN----YGERPLRAVAKDDEGD-----LTKGEVLTGKS--------HMPTPTKLIWFGNSNSLLGNA
    3ir5.1.A  LIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLFIWRSNLLGSSG

    Target    KWSFDV------------------------------VKNTLPRQDAVFCNEWHWTSSCEYADLVFPADSWAEFKLPDATA
    3ir5.1.A  KGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYEK--DDMNT

    Target    SCTNPFLLAFPTTPLKRLYDTRSDYEALALTAKALGELIDEPRMEQYWRGILDGDPTPYLQRIFSGSNATRGITYDELHE
    3ir5.1.A  SDMHPFIHP-LSAAVDPAWEAKSDWEIYKAIAKKFSE-------------------------------------------

    Target    SSKRGVPLLMNMRTYPRSGGWEQRQEDKPWYTATGRLEFYRPEPEFQAAGESLPVWREPVDATFYEPNAILSNAAHPSIA
    3ir5.1.A  --------------------------------------------------------------------------------

    Target    PRAPEDYGVPESQLDVETRQYRNVVRTWAELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVDADWISMLFGPFGDPYR
    3ir5.1.A  --------------------------------------------------------------------------------

    Target    RDPRMPWTGEAYLEINPKDAA
    3ir5.1.A  ---------------------

### Model #03 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.20 | 0.46 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
3ir7.1.A | 31.10 | monomer | 0.00 | BLAST | X-ray | 2.50Å | 0.36 | 90 - 451 | 0.42 | Respiratory nitrate reductase 1 alpha chain

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
6MO.4 | 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
SF4.3 | 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    SWDEATTIAAKTMEDVARTFNGDEGARKLLAQGYHPEMVEVMHGAGVQALKLRGGMPLLGIGRIFGFYRFANMLALLDRK
    3ir7.1.A  --------------------------------------------------------------------------------

    Target    LRPDAPADEILGSRTFDNYAWHTDLPPGHPMVTGSQTVDFDLFSAEHTKLLLIIGMNWICTKMPDGHWIGDARLKGTRVI
    3ir7.1.A  ---------LIGGTCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGSNVPQTRTPDAHFFTEVRYKGTKTV

    Target    VISADYMPTANKADEVIILRPGTDAAFFLGVARELIEKGLYDRAA------VIERTDLPLLVRLDTGERLDARDVIPGYE
    3ir7.1.A  AVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYTDMPMLVMLE------ERD---GYY

    Target    LAALTNYVTLKPDAEIKGNPP---PPPFTAGGQVVP--TELRDAWGDFVWW-----DRATGRPRPV------SRDEVGA-
    3ir7.1.A  AAGRMLRAADLVDALGQENNPEWKTVAFNTNGEMVAPNGSIGFRWGEKGKWNLEQRDGKTGEETELQLSLLGSQDEIAEV

    Target    ---RFDGD-----------PALLGEFEV---ELVDGSTVPVRPAFDL------LKQYLDE-----SFDLRTA------SE
    3ir7.1.A  GFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVYDLTLANYGLERGLNDVNCATSYDDVKAYTPAWAEQ

    Target    VCRVPPQAIQSIARQLAANKRET----LLAAGMGPNHYFQNDLFGRVQFLVAALTDNIGHLGGNVGSYAGNYRGSVFQAM
    3ir7.1.A  ITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHLDMNYRGLINMLIFCGCVGQSGGGWAHYVGQEK---LRPQ

    Target    GQWIAEDPFAIEPDLTKPATVKRYYKAESAHYWNYGERPLRAVAKDDEGDLTKGEVLTGKSHMPTPTKLIWFGNSNSLLG
    3ir7.1.A  TGW---QPLAFALDWQRPA---RHMNSTSYFY------------------------------------------------

    Target    NAKWSFDVVKNTLPRQDAVFCNEWHWTSSCEYADLVFPADSWAEFKLPDATASCTNPFLLAFPTTPLKRLYDTRSDYEAL
    3ir7.1.A  --------------------------------------------------------------------------------

    Target    ALTAKALGELIDEPRMEQYWRGILDGDPTPYLQRIFSGSNATRGITYDELHESSKRGVPLLMNMRTYPRSGGWEQRQEDK
    3ir7.1.A  --------------------------------------------------------------------------------

    Target    PWYTATGRLEFYRPEPEFQAAGESLPVWREPVDATFYEPNAILSNAAHPSIAPRAPEDYGVPESQLDVETRQYRNVVRTW
    3ir7.1.A  --------------------------------------------------------------------------------

    Target    AELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVDADWISMLFGPFGDPYRRDPRMPWTGEAYLEINPKDAA
    3ir7.1.A  -------------------------------------------------------------------------

### Model #04 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.04 | 0.42 ± 0.08

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1r27.4.A | 17.24 | monomer | 0.00 | HHblits | X-ray | 2.00Å | 0.27 | 654 - 769 | 0.14 | Respiratory nitrate reductase 1 alpha chain

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
F3S.5 | Binding site not conserved. | FE3-S4 CLUSTER
F3S.13 | Binding site not conserved. | FE3-S4 CLUSTER
F3S.21 | Binding site not conserved. | FE3-S4 CLUSTER
F3S.29 | Binding site not conserved. | FE3-S4 CLUSTER
MGD.3 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.4 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.11 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.12 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.19 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.20 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.27 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.28 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MO.1 | Binding site not conserved. | MOLYBDENUM ATOM
MO.9 | Binding site not conserved. | MOLYBDENUM ATOM
MO.17 | Binding site not conserved. | MOLYBDENUM ATOM
MO.25 | Binding site not conserved. | MOLYBDENUM ATOM
SF4.2 | 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
SF4.10 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.14 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.15 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.16 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.18 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.22 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.23 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.24 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.26 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.30 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.31 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.32 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    SWDEATTIAAKTMEDVARTFNGDEGARKLLAQGYHPEMVEVMHGAGVQALKLRGGMPLLGIGRIFGFYRFANMLALLDRK
    1r27.4.A  --------------------------------------------------------------------------------

    Target    LRPDAPADEILGSRTFDNYAWHTDLPPGHPMVTGSQTVDFDLFSAEHTKLLLIIGMNWICTKMPDGHWIGDARLKGTRVI
    1r27.4.A  --------------------------------------------------------------------------------

    Target    VISADYMPTANKADEVIILRPGTDAAFFLGVARELIEKGLYDRAAVIERTDLPLLVRLDTGERLDARDVIPGYELAALTN
    1r27.4.A  --------------------------------------------------------------------------------

    Target    YVTLKPDAEIKGNPPPPPFTAGGQVVPTELRDAWGDFVWWDRATGRPRPVSRDEVGARFDGDPALLGEFEVELVDGSTVP
    1r27.4.A  --------------------------------------------------------------------------------

    Target    VRPAFDLLKQYLDESFDLRTASEVCRVPPQAIQSIARQLAANKRETLLAAGMGPNHYFQNDLFGRVQFLVAALTDNIGHL
    1r27.4.A  --------------------------------------------------------------------------------

    Target    GGNVGSYAGNYRGSVFQAMGQWIAEDPFAIEPDLTKPATVKRYYKAESAHYWNYGERPLRAVAKDDEGDLTKGEVLTGKS
    1r27.4.A  --------------------------------------------------------------------------------

    Target    HMPTPTKLIWFGNSNSLLGNAKWSFDVVKNTLPRQDAVFCNEWHWTSSCEYADLVFPADSWAEFKLPDATASCTNPFLLA
    1r27.4.A  --------------------------------------------------------------------------------

    Target    FPTTPLKRLYDTRSDYEALALTAKALGELIDEPRMEQYWRGILDGDPTPYLQRIFSGSNATRGITYDELHESSKRGVPLL
    1r27.4.A  --------------------------------------------------------------------------------

    Target    MNMRTYPRSGGWEQRQEDKPWYTATGRLEFYRPEPEFQAAGESLPVWREPVDAT-------------FYEPNAILSNAAH
    1r27.4.A  -------------NVHELIPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSVKEVIGQKSNGNQEKALNFLTPHQK

    Target    PSIAPRAPED-------YGVPESQLDVETRQYRN-----VVRTWAELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVD
    1r27.4.A  WGIHSTYSDNLLMLTLGRGGPVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVVSQRVPAGMTMMYHAQERI------

    Target    ADWISMLFGPFGDPYRRDPRMPWTGEAYLEINPKDAA
    1r27.4.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.

SWDEATTIAAKTMEDVARTFNGDEGARKLLAQGYHPEMVEVMHGAGVQALKLRGGMPLLGIGRIFGFYRFANMLALLDRKLRPDAPADEILGSRTFDNYA
WHTDLPPGHPMVTGSQTVDFDLFSAEHTKLLLIIGMNWICTKMPDGHWIGDARLKGTRVIVISADYMPTANKADEVIILRPGTDAAFFLGVARELIEKGL
YDRAAVIERTDLPLLVRLDTGERLDARDVIPGYELAALTNYVTLKPDAEIKGNPPPPPFTAGGQVVPTELRDAWGDFVWWDRATGRPRPVSRDEVGARFD
GDPALLGEFEVELVDGSTVPVRPAFDLLKQYLDESFDLRTASEVCRVPPQAIQSIARQLAANKRETLLAAGMGPNHYFQNDLFGRVQFLVAALTDNIGHL
GGNVGSYAGNYRGSVFQAMGQWIAEDPFAIEPDLTKPATVKRYYKAESAHYWNYGERPLRAVAKDDEGDLTKGEVLTGKSHMPTPTKLIWFGNSNSLLGN
AKWSFDVVKNTLPRQDAVFCNEWHWTSSCEYADLVFPADSWAEFKLPDATASCTNPFLLAFPTTPLKRLYDTRSDYEALALTAKALGELIDEPRMEQYWR
GILDGDPTPYLQRIFSGSNATRGITYDELHESSKRGVPLLMNMRTYPRSGGWEQRQEDKPWYTATGRLEFYRPEPEFQAAGESLPVWREPVDATFYEPNA
ILSNAAHPSIAPRAPEDYGVPESQLDVETRQYRNVVRTWAELQQTLHPLQERDPAFRFVFQTPKYRWGAHSTAVDADWISMLFGPFGDPYRRDPRMPWTG
EAYLEINPKDAA

## Table T2:

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 40.77 | monomer | - | BLAST | X-ray | 2.97Å | 0.41 | 0.95 | Nitrite oxidoreductase subunit A
7b04.1.B | 38.92 | monomer | - | HHblits | X-ray | 2.97Å | 0.40 | 0.96 | Nitrite oxidoreductase subunit A
7b04.2.B | 40.77 | monomer | - | BLAST | X-ray | 2.97Å | 0.41 | 0.95 | Nitrite oxidoreductase subunit A
7b04.2.B | 38.92 | monomer | - | HHblits | X-ray | 2.97Å | 0.40 | 0.96 | Nitrite oxidoreductase subunit A
5e7o.1.A | 26.73 | monomer | - | HHblits | X-ray | 2.40Å | 0.34 | 0.78 | DMSO reductase family type II enzyme, molybdopterin subunit
4ydd.1.A | 26.30 | monomer | - | HHblits | X-ray | 1.86Å | 0.34 | 0.78 | DMSO reductase family type II enzyme, molybdopterin subunit
2ivf.1.A | 25.39 | monomer | - | HHblits | X-ray | 1.88Å | 0.32 | 0.80 | ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
2iv2.1.A | 19.92 | monomer | - | HHblits | X-ray | 2.27Å | 0.31 | 0.66 | Formate dehydrogenase H
4ydd.1.A | 30.81 | monomer | - | BLAST | X-ray | 1.86Å | 0.36 | 0.68 | DMSO reductase family type II enzyme, molybdopterin subunit
1aa6.1.A | 19.92 | monomer | - | HHblits | X-ray | 2.30Å | 0.31 | 0.66 | FORMATE DEHYDROGENASE H
5e7o.1.A | 30.81 | monomer | - | BLAST | X-ray | 2.40Å | 0.36 | 0.68 | DMSO reductase family type II enzyme, molybdopterin subunit
7z0t.1.G | 19.92 | monomer | - | HHblits | EM | NA | 0.31 | 0.66 | Formate dehydrogenase H
1fdo.1.A | 19.92 | monomer | - | HHblits | X-ray | 2.80Å | 0.31 | 0.66 | FORMATE DEHYDROGENASE H
3ir5.1.A | 23.32 | monomer | - | HHblits | X-ray | 2.30Å | 0.32 | 0.62 | Respiratory nitrate reductase 1 alpha chain
1r27.4.A | 23.52 | monomer | - | HHblits | X-ray | 2.00Å | 0.32 | 0.62 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 23.52 | monomer | - | HHblits | X-ray | 2.50Å | 0.32 | 0.62 | Respiratory nitrate reductase 1 alpha chain
7bkb.1.F | 21.71 | monomer | - | HHblits | EM | NA | 0.31 | 0.65 | Formate dehydrogenase
3egw.1.A | 23.32 | monomer | - | HHblits | X-ray | 1.90Å | 0.32 | 0.62 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 23.52 | monomer | - | HHblits | X-ray | 1.90Å | 0.32 | 0.62 | Respiratory nitrate reductase 1 alpha chain
3ir6.1.A | 23.32 | monomer | - | HHblits | X-ray | 2.80Å | 0.32 | 0.62 | Respiratory nitrate reductase 1 alpha chain
1e60.1.A | 20.65 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.60 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e5v.2.A | 20.82 | monomer | - | HHblits | X-ray | 2.40Å | 0.30 | 0.60 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
4dmr.1.A | 20.78 | monomer | - | HHblits | X-ray | 1.90Å | 0.30 | 0.60 | DMSO REDUCTASE
1e18.1.A | 20.78 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.60 | DMSO REDUCTASE.
2ivf.1.A | 39.42 | monomer | - | BLAST | X-ray | 1.88Å | 0.39 | 0.30 | ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
3egw.1.A | 31.66 | monomer | - | BLAST | X-ray | 1.90Å | 0.36 | 0.42 | Respiratory nitrate reductase 1 alpha chain
6zr2.1.G | 11.46 | monomer | - | HHblits | EM | 3.10Å | 0.25 | 0.39 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
3ir7.1.A | 31.10 | monomer | - | BLAST | X-ray | 2.50Å | 0.36 | 0.42 | Respiratory nitrate reductase 1 alpha chain
3ir5.1.A | 31.10 | monomer | - | BLAST | X-ray | 2.30Å | 0.36 | 0.42 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 31.10 | monomer | - | BLAST | X-ray | 1.90Å | 0.36 | 0.42 | Respiratory nitrate reductase 1 alpha chain
1r27.4.A | 31.10 | monomer | - | BLAST | X-ray | 2.00Å | 0.36 | 0.42 | Respiratory nitrate reductase 1 alpha chain
7ak5.1.G | 11.46 | monomer | - | HHblits | EM | NA | 0.25 | 0.39 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
3ir6.1.A | 31.10 | monomer | - | BLAST | X-ray | 2.80Å | 0.36 | 0.42 | Respiratory nitrate reductase 1 alpha chain
7ak6.1.G | 11.46 | monomer | - | HHblits | EM | NA | 0.25 | 0.39 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6g72.1.G | 11.46 | monomer | - | HHblits | EM | NA | 0.25 | 0.39 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7zd6.1.4 | 17.02 | monomer | - | HHblits | EM | NA | 0.30 | 0.12 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6qc5.1.C | 17.02 | monomer | - | HHblits | EM | NA | 0.30 | 0.12 | NADH:ubiquinone oxidoreductase core subunit S1
6qcf.1.C | 17.02 | monomer | - | HHblits | EM | NA | 0.30 | 0.12 | NADH:ubiquinone oxidoreductase core subunit S1
5gpn.24.A | 15.96 | monomer | - | HHblits | EM | NA | 0.29 | 0.12 | NADH-ubiquinone oxidoreductase 75 kDa subunit
3m9s.1.C | 21.79 | monomer | - | HHblits | X-ray | 4.50Å | 0.29 | 0.10 | NADH-quinone oxidoreductase subunit 3
2fug.2.C | 21.79 | monomer | - | HHblits | X-ray | 3.30Å | 0.29 | 0.10 | NADH-quinone oxidoreductase chain 3
6zjl.1.C | 21.79 | monomer | - | HHblits | EM | NA | 0.29 | 0.10 | NADH-quinone oxidoreductase subunit 3
6q8o.1.C | 21.79 | monomer | - | HHblits | X-ray | 3.61Å | 0.29 | 0.10 | NADH-quinone oxidoreductase subunit 3
6zjy.1.C | 21.79 | monomer | - | HHblits | EM | NA | 0.29 | 0.10 | NADH-quinone oxidoreductase subunit 3
1r27.4.A | 17.24 | monomer | - | HHblits | X-ray | 2.00Å | 0.27 | 0.14 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 17.39 | monomer | - | HHblits | X-ray | 1.90Å | 0.27 | 0.14 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 17.24 | monomer | - | HHblits | X-ray | 1.90Å | 0.27 | 0.14 | Respiratory nitrate reductase 1 alpha chain
3ir6.1.A | 17.54 | monomer | - | HHblits | X-ray | 2.80Å | 0.27 | 0.14 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 17.39 | monomer | - | HHblits | X-ray | 2.50Å | 0.27 | 0.14 | Respiratory nitrate reductase 1 alpha chain
3ir5.1.A | 17.24 | monomer | - | HHblits | X-ray | 2.30Å | 0.27 | 0.14 | Respiratory nitrate reductase 1 alpha chain

The table above shows the top 50 filtered templates. A further 199 templates were found which were considered to be less suitable for modelling than the filtered list.
1aa6.1.A, 1dms.1.A, 1e18.1.A, 1e5v.2.A, 1e60.1.A, 1eiw.1.A, 1eu1.1.A, 1fdo.1.A, 1g8j.1.A, 1g8k.1.A, 1h0h.1.A, 1ici.1.A, 1jeo.1.A, 1kqf.1.A, 1m2g.1.A, 1m2h.1.A, 1m2j.1.A, 1m2k.1.A, 1m2n.1.A, 1m2n.1.B, 1ma3.1.A, 1ogy.1.A, 1q16.1.A, 1r27.4.A, 1s5p.1.A, 1s7g.1.A, 1s7g.1.B, 1s7g.1.C, 1s7g.1.D, 1s7g.1.E, 1tmo.1.A, 1tzb.1.A, 1tzb.1.B, 1x94.1.A, 1x94.1.B, 1yc5.1.A, 2a3n.1.A, 2b4y.1.A, 2b4y.3.A, 2e7z.1.A, 2h2i.1.A, 2h4h.1.A, 2h59.1.B, 2i2w.1.A, 2i2w.2.B, 2iv2.1.A, 2ivf.1.A, 2nya.1.A, 2nyr.1.A, 2nyr.1.B, 2v3v.1.A, 2v45.1.A, 2vpx.1.D, 2vpz.1.A, 2x3y.1.A, 2x48.1.A, 2x48.2.A, 2x48.3.A, 3egw.1.A, 3etn.1.A, 3eua.1.A, 3fj1.1.A, 3hba.1.A, 3hba.1.B, 3ir5.1.A, 3ir6.1.A, 3ir7.1.A, 3jr3.1.A, 3jwp.1.A, 3k35.1.A, 3knz.1.A, 3o5a.1.A, 3pki.1.A, 3riy.2.A, 3sho.1.A, 3sho.1.C, 3u31.1.A, 3zg6.1.A, 4aay.1.A, 4bv2.3.A, 4dmr.1.A, 4g1c.1.A, 4g1c.2.A, 4hda.1.A, 4hda.2.A, 4ivn.1.A, 4s12.1.A, 4s12.2.A, 4s12.2.B, 4twi.1.A, 4twj.1.A, 4utn.1.A, 4utn.2.A, 4v4c.1.A, 4ydd.1.A, 5bwl.1.A, 5e7o.1.A, 5gpn.24.A, 5ltz.1.A, 5lu5.1.A, 5lu6.1.A, 5lu7.1.A, 5mf6.1.A, 5nqd.1.A, 5o31.1.8, 5oj7.1.A, 5ojn.1.A, 5t5i.1.B, 5x16.1.A, 5xhs.1.A, 5xtb.1.L, 5y2f.1.A, 6aco.1.A, 6acp.1.A, 6btm.1.B, 6cz7.1.A, 6enx.1.A, 6eo0.1.A, 6eqs.3.A, 6f0k.1.B, 6fky.1.A, 6fky.2.A, 6flg.1.A, 6g72.1.G, 6gcs.1.A, 6ljk.1.A, 6ljm.1.A, 6lod.1.B, 6qc5.1.C, 6qcf.1.C, 6rfq.1.A, 6rfs.1.A, 6rxj.1.A, 6rxm.1.A, 6rxm.2.A, 6rxm.3.A, 6rxm.4.A, 6rxm.5.A, 6rxm.6.A, 6rxo.1.A, 6rxo.2.A, 6rxp.2.A, 6rxq.4.A, 6rxs.1.A, 6s6y.1.B, 6sdr.1.A, 6sdv.1.A, 6tg9.1.A, 6x89.1.H, 6xvg.3.A, 6yj4.1.G, 6ziy.1.C, 6zjn.1.C, 6zk9.1.C, 6zr2.1.G, 7a23.1.O, 7ak5.1.G, 7ak6.1.G, 7aqr.1.F, 7ar7.1.G, 7ar8.1.G, 7arc.1.F, 7b04.1.B, 7b04.2.B, 7bkb.1.F, 7bkb.1.L, 7cl0.1.A, 7dgr.10.A, 7e5z.1.A, 7en5.1.A, 7en6.1.A, 7en6.1.B, 7en6.1.C, 7en6.1.D, 7kqa.1.A, 7kqa.1.B, 7l5i.1.A, 7l5s.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, 7v2c.1.L, 7vw6.1.A, 7vxu.1.L, 7z0t.1.G, 7zd6.1.4, 7zm7.1.I, 8b9z.1.G, 8ba0.1.G, 8bqg.1.A, 8e73.55.A, 8e9g.1.G