|  | SWISS-MODEL Homology Modelling Report

## Model Building Report

This document lists the results for the homology modelling project "13_July_SF_Bin2_scaffold_20759_c1_1114-3024_1" submitted to SWISS-MODEL workspace on March 29, 2023, 7:36 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 301 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 | 0.69 | 0.64 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 41.23 | monomer | 0.00 | BLAST | X-ray | 2.97Å | 0.40 | 1 - 624 | 0.97 | 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    LARDIAKVPGTTLFAIGMGPNQFFNNDNKDRTQFLLAALTGNIGKIAGNIGSYAGNYRVAMFN-------GVPQYIAENP
    7b04.1.B  LAKDIATIKPVAIH-YGEGVNHYFHATLMNRSYYLPVMLTGNVGYFGSGSHTWAGNYKAGNFQASKWSGPGFYGWVAEDV

    Target    FDIELD---GAKPARPKLYWRAEPAHYYNHEDHPL-----KMGKTMITGKTHMPTPTKSLWFANANSILGNVKWHFNTVV
    7b04.1.B  FKPNLDPYASAKDLNIKGRALDEEVAYWNHSERPLIVNTPKYGRKVFTGKTHMPSPTKVLWFTNVN-LINNAKHVYQMLK

    Target    NVLPKMEMIAVQEWWWSTSCEWADIVFAVDAWSELKHPDMCSSVTNPFLTVFPRTPLERPFDTRGDIECLDLVGKQLAKR
    7b04.1.B  NVNPNIEQIMSTDIEITGSIEYADFAFPANSWVEFQEFEITNSCSNPFIQIWGKTGITPVYESKDDVKILAGMASKLGEL

    Target    TGDRRFADMWKFVEEKKVEVYLQRILDHSSNTKGFKFPELEEKAKKGIP--ALMMTRTNPKTVGYEQVYDSRPWYTKTGR
    7b04.1.B  LRDKRFEDNWKFAIEGRASVYINRLLDGSTTMKGYTCEDILN-GKYGEPGVAMLLFRTYPRHPFWEQVHESLPFYTPTGR

    Target    LEFYREEDEFIEAGENLPVHREPIDSTFYEPNVIVAPAHPFIKAKGPEAYGVKVDDFDNETRQGRNIVKTWEETKKTVHP
    7b04.1.B  LQAYNDEPEIIEYGENFIVHREGPEATPYLPNAIVS-TNPYIR---PDDYGIPENAEYWEDRTVRNIKKSWEETKKTKNF

    Target    LAKDGYKFVFHTPKYRHGAHTMPVDTDMVAMLFGPFGDIYRHDKRQPFAAEGYVDIHPDDAKALNIEDGDYVWIDSDPSD
    7b04.1.B  LWEKGYHFYCVTPKSRHTVHSQWAVTDWNFIWNNNFGDPYRMDKRMPGVGEHQIHIHPQAARDLGIEDGDYVYVDANPAD

    Target    RPFRGWQKNDKDYKFSRLLCRARYYPGTPRGITRMWFNMYGATPGSVEGHESRKDGLAKNPRTGYQAMFRSGSHQSATRG
    7b04.1.B  RPYEGWKPNDSFYKVSRLMLRAKYNPAYPYNCTMMKHSAWISSDKTVQAHETRPDGRALSP-SGYQSSFRYGSQQSITRD

    Target    WLKPTWMTDSLVRKELFGHAVNKGFLPDVHCPTGAPREAIVKITKAEPGGLNAKGLWRPAALGLRPKYENDKMKDYLAGK
    7b04.1.B  WSMPMHQLDSLFHKAKIGMKFIFGFEADNHCINTVPKETLVKITKAENGGMGGKGVWDPVKTGYTAGNENDFMKKFLNGE

    Target    FTLAANPKKGGKK
    7b04.1.B  L------------

### Model #02 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer (matching prediction) | None | 0.41 | 0.48 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1r27.4.A | 21.88 | homo-dimer | - | HHblits | X-ray | 2.00Å | 0.31 | 1 - 595 | 0.77 | 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    LARDIAKVP----GTTLFAIGMGPNQFFNNDNKDRTQFLLAALTGNIGKIAGNIGSYAGNYRVAMFNGVPQY--IAE--N
    1r27.4.A  IAREFADNADKTHGRSMIIVGAGLNHWYHLDMNYRGLINMLIFCGCVGQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQR

    Target    PF----------------------DIELDGAKPARPKLYWRA--------EPAHYYN----HEDHPL-----------K-
    1r27.4.A  PARHMNSTSYFYNHSSQWRYETVTAEELLSP-MADKSRYTGHLIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNP

    Target    ---MGKTMITGKT--------HMPTPTKSLWFANANSILGNVKWHFNT--------------------------------
    1r27.4.A  VDYTVKSLKEGSIRFAAEQPENGKNHPRNLFIWRSNLLGSSG--KGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQ

    Target    VVNVLPKMEMIAVQEWWWSTSCEWADIVFAVDAWSELKHPDMCSSVTNPFLTVFPRTPLERPFDTRGDIECLDLVGKQLA
    1r27.4.A  DNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYEKD--DMNTSDMHPFIHPLS-AAVDPAWEAKSDWEIYKAIAKKFS

    Target    KRTG----DRR----F---------------ADMWK----------------------------FVE-------------
    1r27.4.A  EVCVGHLGKETDIVTLPIQHDSAAELAQPLDVKDWKKGECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGNGGK

    Target    -----EKKVEVY-------------------------LQRILDHSSNTKGF----KFPELEEKAKKGIPALMMT------
    1r27.4.A  GIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAIDAAEMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKI

    Target    -----R------------------TNPKTVGYEQVYDSRPWYTKTGRLEFYREEDEFIEAGENLPVHREPIDSTFYEPNV
    1r27.4.A  RFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYTNVHELIPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSVKE--

    Target    IVAPAHPFIKAKGPEAYGVKVDDFDNETRQGRNIVKTWEETKKTVHPLAKDGYKFVFHTPKYRHGAHTMPVDTDMVAMLF
    1r27.4.A  -------------------------------------VIGQ----KSNGNQEKALNFLTPHQKWGIHSTYSDNLLMLTL-

    Target    GPFGDIYRHDKRQPFAAEGYVDIHPDDAKALNIEDGDYVWIDSDPSDRPFRGWQKNDKDYKFSRLLCRARYYPGTPRGIT
    1r27.4.A  --------------GRGGPVVWLSEADAKDLGIADNDWIEVFNSN-----------------GALTARAVVSQRVPAGMT

    Target    RMWFNMYGATPGSVEGHESRKDGLAKNPRTGYQAMFRSGSHQSATRGWLKPTWMTDSLVRKELFGHAVNKGFLPDVHCPT
    1r27.4.A  MMYHAQERI------------VNLPGSEIT----QQRGGIHNSVTRITPKPTHMIGGY---------AHLAYGFNYYGTV

    Target    GAPREAIVKITKAEPGGLNAKGLWRPAALGLRPKYENDKMKDYLAGKFTLAANPKKGGKK
    1r27.4.A  GSNRDEFVVVRKMKNIDWL-----------------------------------------

### Model #03 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.28 | 0.40 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7p63.1.C | 12.82 | monomer | 0.00 | HHblits | EM | - | 0.26 | 1 - 504 | 0.55 | NADH-quinone oxidoreductase

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
3PE.15 | Binding site not conserved. | 1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.16 | Binding site not conserved. | 1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.18 | Binding site not conserved. | 1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.19 | Binding site not conserved. | 1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.20 | Binding site not conserved. | 1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.21 | Binding site not conserved. | 1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.24 | Binding site not conserved. | 1,2-Distearoyl-sn-glycerophosphoethanolamine
3PE.25 | Binding site not conserved. | 1,2-Distearoyl-sn-glycerophosphoethanolamine
CA.9 | Binding site not conserved. | CALCIUM ION
DCQ.10 | Binding site not conserved. | 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
FES.4 | Binding site not conserved. | FE2/S2 (INORGANIC) CLUSTER
FES.8 | Binding site not conserved. | FE2/S2 (INORGANIC) CLUSTER
FMN.2 | Binding site not conserved. | FLAVIN MONONUCLEOTIDE
LFA.14 | Binding site not conserved. | EICOSANE
LFA.17 | Binding site not conserved. | EICOSANE
LFA.22 | Binding site not conserved. | EICOSANE
LFA.23 | Binding site not conserved. | EICOSANE
NAI.3 | Binding site not conserved. | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
SF4.1 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.5 | 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
SF4.11 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.12 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.13 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    LARDIAKVPGTTLFAIGMGPNQFFNNDNKDRTQFLLAALTGNIGKIAGNIGSYAGNYRVAMFNGVPQYIAENPFDIELDG
    7p63.1.C  IVQALAGAKKP-LIISGTNAG----SLEVIQAAANVAKALKGRGADVGIT-MIARSVNSM---GLGI----------MGG

    Target    AKPARPKLYWRAEPAHYYNHEDHPLKMGKTMITGKTHMPTPTKSLWFANANSILGNVKWHFNTVVNVLPKMEMIAVQEWW
    7p63.1.C  ---------------------GSLEEALTEL------ETGRADAVVVLE-NDLHRH--ASATRVNAALAKAPLVMVVDHQ

    Target    WSTSCEWADIVFAVDAWSELKHPDMCSSVTNP--FLTVFPRTPLERPF-----DTRGDIECLDLVGKQLAKRTGDRRFAD
    7p63.1.C  RTAIMENAHLVLSAASFAESD-----GTVINNEGRAQRFF-QVYDPAYYDSKTVMLESWRWLHS----LHSTLLSRE---

    Target    MWKFVEEKKVEVYLQRILDHSSNTKGFKFPELEEKAK----------------------KGIPALMMTRT----------
    7p63.1.C  -VDWT---QLDHVIDAVVAKIPELAGIKDAAPDATFRIRGQKLAREPHRYSGRTAMRANISVHEPRQPQDIDTMFTFSME

    Target    -------NPKT-V-GYEQVY-----DSRPWYTKTGRLEFYREEDEFIEAG-ENLPVHREPIDSTFYEPNVIVAPAHPFIK
    7p63.1.C  GNNQPTAHRSQVPFAWAPGWNSPQAWNKFQDEVGGKLRFGDPGVRLFETSENGLDYFTSVPA------------------

    Target    AKGPEAYGVKVDDFDNETRQGRNIVKTWEETKKTVHPLAKDGYKFVFHTPKYRHGAHTMPVDTDMVAMLFGPFGDIYRHD
    7p63.1.C  ------------------------------------RFQPQDGKWRIAPYYHLFGSDELSQRAPVFQS------------

    Target    KRQPFAAEGYVDIHPDDAKALNIEDGDYVWIDSDPSDRPFRGWQKNDKDYKFSRLLCRARYYPGTPRGITRMWFNMYGAT
    7p63.1.C  ----RMPQPYIKLNPADAAKLGVNAGTRVSFSYDG-----------------NTVTLPVEIAEGLTAGQVGLPMGMSG--

    Target    PGSVEGHESRKDGLAKNPRTGYQAMFRSGSHQSATRGWLKPTWMTDSLVRKELFGHAVNKGFLPDVHCPTGAPREAIVKI
    7p63.1.C  --------------------------------------------------------------------------------

    Target    TKAEPGGLNAKGLWRPAALGLRPKYENDKMKDYLAGKFTLAANPKKGGKK
    7p63.1.C  --------------------------------------------------

### Model #04 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.14 | 0.35 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
2fug.2.C | 18.56 | monomer | 0.00 | HHblits | X-ray | 3.30Å | 0.28 | 144 - 505 | 0.31 | 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    LARDIAKVPGTTLFAIGMGPNQFFNNDNKDRTQFLLAALTGNIGKIAGNIGSYAGNYRVAMFNGVPQYIAENPFDIELDG
    2fug.2.C  --------------------------------------------------------------------------------

    Target    AKPARPKLYWRAEPAHYYNHEDHPLKMGKTMITGKTHMPTPTKSLWFANANSILGNVKWHFNTVVNVLPKMEMIAVQEWW
    2fug.2.C  ---------------------------------------------------------------PEEALKGKRFVVMHLSH

    Target    WSTSC-EWADIVFAVDAWSELKHPDMCSSVTNPFLTV-FPRTPLERPFDTRGDIECLDLVGKQLAKRTGDRRFADMWKFV
    2fug.2.C  LHPLAERYAHVVLPAPTFYEKR-----GHLVNLEGRVLPLSPAPIENGEAEGALQVLAL----LAEALGVRP-----PFR

    Target    EEKKVEVYLQRILDHSSNTKGFKFPELEEKAKKGIPALMMTRTNPKTVGYEQVYDSRPWYTKTGRLEFYREEDEFIEAGE
    2fug.2.C  ---LHLEAQK---------------ALK---------------------------ARKVPEAMGRLSFRLKEL-------

    Target    NLPVHREPIDSTFYEPNVIVAPAHPFIKAKGPEAYGVKVDDFDNETRQGRNIVKTWEETKKTVHPLAKDGYKFVFHTPKY
    2fug.2.C  --R----P----------------------------------------------------------KERKGAFYLRPTMW

    Target    RHGAHTMPVDTDMVAMLFGPFGDIYRHDKRQPFAAEGYVDIHPDDAKALNIEDGDYVWIDSDPSDRPFRGWQKNDKDYKF
    2fug.2.C  KAHQAVG-----KA-------------Q----EAARAELWAHPETARAEALPEGAQVAVETPF-----------------

    Target    SRLLCRARYYPGTPRGITRMWFNMYGATPGSVEGHESRKDGLAKNPRTGYQAMFRSGSHQSATRGWLKPTWMTDSLVRKE
    2fug.2.C  GRVEARVVHREDVPKGHLYLSALGPAAG----------------------------------------------------

    Target    LFGHAVNKGFLPDVHCPTGAPREAIVKITKAEPGGLNAKGLWRPAALGLRPKYENDKMKDYLAGKFTLAANPKKGGKK
    2fug.2.C  ------------------------------------------------------------------------------

### Model #05 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.13 | 0.44 ± 0.06

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
2ivf.1.A | 30.93 | monomer | 0.00 | BLAST | X-ray | 1.88Å | 0.36 | 147 - 342 | 0.31 | ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
ACT.2 | Not biologically relevant. | ACETATE ION
ACT.7 | Not biologically relevant. | ACETATE ION
F3S.15 | Binding site not conserved. | FE3-S4 CLUSTER
GOL.3 | Not biologically relevant. | GLYCEROL
GOL.4 | Not biologically relevant. | GLYCEROL
GOL.5 | Not biologically relevant. | GLYCEROL
GOL.6 | Not biologically relevant. | GLYCEROL
GOL.12 | Not biologically relevant. | GLYCEROL
GOL.14 | Not biologically relevant. | GLYCEROL
GOL.19 | Not biologically relevant. | GLYCEROL
GOL.20 | Not biologically relevant. | GLYCEROL
HEM.21 | Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
MD1.11 | 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
MES.1 | Binding site not conserved. | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
MGD.10 | 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.9 | Binding site not conserved. | MOLYBDENUM ATOM
PO4.13 | Not biologically relevant. | PHOSPHATE ION
SF4.8 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.16 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.17 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.18 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    LARDIAKVPGTTLFAIGMGPNQFFNNDNKDRTQFLLAALTGNIGKIAGNIGSYAGNYRVAMFNGVPQYIAENPFDIELDG
    2ivf.1.A  --------------------------------------------------------------------------------

    Target    AKPARPKLYWRAEPAHYYNHEDHPLKMGKTMITGKTHMPTPTKSLWFANANSILGNVKWHFNTVVNVLPKMEMIAVQEWW
    2ivf.1.A  ------------------------------------------------------------------LFPKLKMIFALETR

    Target    WSTSCEWADIVFAVDAWSELKHPDMCSSVTNPFLTVFPRTPLERPFDTRGDIECLDLVGKQLAKRTG-------------
    2ivf.1.A  MSSSAMYADIVLPC-AWYYEKHEMTTPCSGNPFFTFVDRS-VAPPGECREEWDAIALILKKVGERAAARGLTEFNDHNGR

    Target    DRRFADMW-KFVEEKKV---EVYLQRILDHSSNTKGFKFPELEEKAKK-GIPALMMTRTNPKTVGYEQVYD-SRPWY---
    2ivf.1.A  KRRYDELYKKFTMDGHLLTNEDCLKEMVDINRAVGVFAKDYTYEKFKKEGQTRFLSMGTGVSRYAHANEVDVTKPIYPMR

    Target    ----------TKTGRLEFYREEDEFIEAGENLPVHRE--------PIDSTFYEPNVIVAPAHPFIKAKGPEAYGVKVDDF
    2ivf.1.A  WHFDDKKVFPTHTRRAQFYLDHDWYLEAGESLPTHKDTPMVGGDHPFKITGGHPRVSIHSTH------------------

    Target    DNETRQGRNIVKTWEETKKTVHPLAKDGYKFVFHTPKYRHGAHTMPVDTDMVAMLFGPFGDIYRHDKRQPFAAEGYVDIH
    2ivf.1.A  --------------------------------------------------------------------------------

    Target    PDDAKALNIEDGDYVWIDSDPSDRPFRGWQKNDKDYKFSRLLCRARYYPGTPRGITRMWFNMYGATPGSVEGHESRKDGL
    2ivf.1.A  --------------------------------------------------------------------------------

    Target    AKNPRTGYQAMFRSGSHQSATRGWLKPTWMTDSLVRKELFGHAVNKGFLPDVHCPTGAPREAIVKITKAEPGGLNAKGLW
    2ivf.1.A  --------------------------------------------------------------------------------

    Target    RPAALGLRPKYENDKMKDYLAGKFTLAANPKKGGKK
    2ivf.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.

LARDIAKVPGTTLFAIGMGPNQFFNNDNKDRTQFLLAALTGNIGKIAGNIGSYAGNYRVAMFNGVPQYIAENPFDIELDGAKPARPKLYWRAEPAHYYNH
EDHPLKMGKTMITGKTHMPTPTKSLWFANANSILGNVKWHFNTVVNVLPKMEMIAVQEWWWSTSCEWADIVFAVDAWSELKHPDMCSSVTNPFLTVFPRT
PLERPFDTRGDIECLDLVGKQLAKRTGDRRFADMWKFVEEKKVEVYLQRILDHSSNTKGFKFPELEEKAKKGIPALMMTRTNPKTVGYEQVYDSRPWYTK
TGRLEFYREEDEFIEAGENLPVHREPIDSTFYEPNVIVAPAHPFIKAKGPEAYGVKVDDFDNETRQGRNIVKTWEETKKTVHPLAKDGYKFVFHTPKYRH
GAHTMPVDTDMVAMLFGPFGDIYRHDKRQPFAAEGYVDIHPDDAKALNIEDGDYVWIDSDPSDRPFRGWQKNDKDYKFSRLLCRARYYPGTPRGITRMWF
NMYGATPGSVEGHESRKDGLAKNPRTGYQAMFRSGSHQSATRGWLKPTWMTDSLVRKELFGHAVNKGFLPDVHCPTGAPREAIVKITKAEPGGLNAKGLW
RPAALGLRPKYENDKMKDYLAGKFTLAANPKKGGKK

## Table T2:

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 41.23 | monomer | - | BLAST | X-ray | 2.97Å | 0.40 | 0.97 | Nitrite oxidoreductase subunit A
7b04.1.B | 39.51 | monomer | - | HHblits | X-ray | 2.97Å | 0.39 | 0.97 | Nitrite oxidoreductase subunit A
7b04.2.B | 41.23 | monomer | - | BLAST | X-ray | 2.97Å | 0.40 | 0.97 | Nitrite oxidoreductase subunit A
7b04.2.B | 39.51 | monomer | - | HHblits | X-ray | 2.97Å | 0.39 | 0.97 | Nitrite oxidoreductase subunit A
5e7o.1.A | 24.62 | monomer | - | HHblits | X-ray | 2.40Å | 0.32 | 0.72 | DMSO reductase family type II enzyme, molybdopterin subunit
4ydd.1.A | 24.40 | monomer | - | HHblits | X-ray | 1.86Å | 0.32 | 0.72 | DMSO reductase family type II enzyme, molybdopterin subunit
1r27.4.A | 21.88 | homo-dimer | - | HHblits | X-ray | 2.00Å | 0.31 | 0.77 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 22.22 | homo-dimer | 0.10 | HHblits | X-ray | 1.90Å | 0.31 | 0.76 | Respiratory nitrate reductase 1 alpha chain
3ir5.1.A | 22.09 | monomer | - | HHblits | X-ray | 2.30Å | 0.31 | 0.77 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 21.88 | monomer | - | HHblits | X-ray | 1.90Å | 0.31 | 0.77 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 21.88 | monomer | - | HHblits | X-ray | 2.50Å | 0.31 | 0.77 | Respiratory nitrate reductase 1 alpha chain
3ir6.1.A | 22.06 | monomer | - | HHblits | X-ray | 2.80Å | 0.31 | 0.76 | Respiratory nitrate reductase 1 alpha chain
1e60.1.A | 20.15 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.62 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e18.1.A | 20.45 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.62 | DMSO REDUCTASE.
1dms.1.A | 20.20 | monomer | - | HHblits | X-ray | 1.88Å | 0.30 | 0.62 | DMSO REDUCTASE
4dmr.1.A | 20.45 | monomer | - | HHblits | X-ray | 1.90Å | 0.30 | 0.62 | DMSO REDUCTASE
1e5v.2.A | 20.51 | monomer | - | HHblits | X-ray | 2.40Å | 0.30 | 0.62 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
1aa6.1.A | 20.65 | monomer | - | HHblits | X-ray | 2.30Å | 0.31 | 0.58 | FORMATE DEHYDROGENASE H
1fdo.1.A | 20.65 | monomer | - | HHblits | X-ray | 2.80Å | 0.31 | 0.58 | FORMATE DEHYDROGENASE H
2iv2.1.A | 20.65 | monomer | - | HHblits | X-ray | 2.27Å | 0.31 | 0.58 | Formate dehydrogenase H
2ivf.1.A | 21.18 | monomer | - | HHblits | X-ray | 1.88Å | 0.30 | 0.53 | ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
7z0t.1.G | 20.65 | monomer | - | HHblits | EM | NA | 0.31 | 0.58 | Formate dehydrogenase H
7p63.1.C | 12.82 | monomer | - | HHblits | EM | NA | 0.26 | 0.55 | NADH-quinone oxidoreductase
7nz1.1.E | 12.82 | monomer | - | HHblits | EM | NA | 0.26 | 0.55 | NADH-quinone oxidoreductase subunit G
7p61.1.C | 12.82 | monomer | - | HHblits | EM | NA | 0.26 | 0.55 | NADH-quinone oxidoreductase
4ydd.1.A | 25.94 | monomer | - | BLAST | X-ray | 1.86Å | 0.34 | 0.50 | DMSO reductase family type II enzyme, molybdopterin subunit
5e7o.1.A | 25.94 | monomer | - | BLAST | X-ray | 2.40Å | 0.33 | 0.50 | DMSO reductase family type II enzyme, molybdopterin subunit
6q8o.1.C | 18.56 | monomer | - | HHblits | X-ray | 3.61Å | 0.28 | 0.31 | NADH-quinone oxidoreductase subunit 3
3m9s.1.C | 18.56 | monomer | - | HHblits | X-ray | 4.50Å | 0.28 | 0.31 | NADH-quinone oxidoreductase subunit 3
6zjn.1.C | 18.56 | monomer | - | HHblits | EM | NA | 0.28 | 0.31 | NADH-quinone oxidoreductase subunit 3
6zjl.1.C | 18.56 | monomer | - | HHblits | EM | NA | 0.28 | 0.31 | NADH-quinone oxidoreductase subunit 3
6ziy.1.C | 18.56 | monomer | - | HHblits | EM | NA | 0.28 | 0.31 | NADH-quinone oxidoreductase subunit 3
6zjy.1.C | 18.56 | monomer | - | HHblits | EM | NA | 0.28 | 0.31 | NADH-quinone oxidoreductase subunit 3
2fug.2.C | 18.56 | monomer | - | HHblits | X-ray | 3.30Å | 0.28 | 0.31 | NADH-quinone oxidoreductase chain 3
7ak5.1.G | 15.23 | monomer | - | HHblits | EM | NA | 0.27 | 0.31 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6zr2.1.G | 16.24 | monomer | - | HHblits | EM | 3.10Å | 0.28 | 0.31 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7ak6.1.G | 16.24 | monomer | - | HHblits | EM | NA | 0.28 | 0.31 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6g72.1.G | 16.24 | monomer | - | HHblits | EM | NA | 0.28 | 0.31 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7zd6.1.4 | 15.43 | monomer | - | HHblits | EM | NA | 0.27 | 0.30 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6zk9.1.C | 15.51 | monomer | - | HHblits | EM | NA | 0.27 | 0.29 | NADH:ubiquinone oxidoreductase core subunit S1
7qsd.1.G | 14.89 | monomer | - | HHblits | EM | NA | 0.27 | 0.30 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7v2c.1.L | 14.97 | monomer | - | HHblits | EM | NA | 0.27 | 0.29 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7dgr.10.A | 15.43 | monomer | - | HHblits | EM | NA | 0.27 | 0.30 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
2ivf.1.A | 30.93 | monomer | - | BLAST | X-ray | 1.88Å | 0.36 | 0.31 | ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
6qcf.1.C | 15.43 | monomer | - | HHblits | EM | NA | 0.27 | 0.30 | NADH:ubiquinone oxidoreductase core subunit S1
6qc5.1.C | 15.43 | monomer | - | HHblits | EM | NA | 0.27 | 0.30 | NADH:ubiquinone oxidoreductase core subunit S1
5o31.1.8 | 15.43 | monomer | - | HHblits | EM | 4.13Å | 0.27 | 0.30 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7vxu.1.L | 15.51 | monomer | - | HHblits | EM | NA | 0.27 | 0.29 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
5gpn.24.A | 16.04 | monomer | - | HHblits | EM | NA | 0.27 | 0.29 | NADH-ubiquinone oxidoreductase 75 kDa subunit
5xtb.1.L | 15.43 | monomer | - | HHblits | EM | NA | 0.27 | 0.30 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

The table above shows the top 50 filtered templates. A further 205 templates were found which were considered to be less suitable for modelling than the filtered list.
1aa6.1.A, 1cz4.1.A, 1cz5.1.A, 1dms.1.A, 1e18.1.A, 1e5v.2.A, 1e60.1.A, 1eu1.1.A, 1fdo.1.A, 1g8j.1.A, 1g8k.1.A, 1h0h.1.A, 1kqf.1.A, 1ogy.1.A, 1q16.1.A, 1r27.4.A, 1tmo.1.A, 1uhd.1.B, 1uhe.1.B, 1wlf.1.A, 1yfb.1.A, 1yfb.1.B, 1yle.1.A, 1ysf.1.A, 1ysf.1.B, 1z0r.1.B, 2e7z.1.A, 2eeo.1.B, 2fy9.1.A, 2iv2.1.A, 2ivf.1.A, 2k1n.1.C, 2k1n.1.D, 2k1n.1.E, 2k1n.1.F, 2ki8.1.A, 2l66.1.A, 2mrn.1.A, 2mru.1.A, 2mru.1.B, 2nya.1.A, 2pjh.1.B, 2ro3.1.A, 2ro4.1.A, 2ro5.1.A, 2v3v.1.A, 2v45.1.A, 2vpx.1.D, 2vpz.1.A, 2yuj.1.A, 3egw.1.A, 3hu1.1.A, 3hu2.1.A, 3ir5.1.A, 3ir6.1.A, 3ir7.1.A, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3pjy.1.A, 3pjy.1.B, 3plx.1.B, 3qc8.1.A, 3qq7.1.A, 3qq8.1.A, 3qwz.1.A, 3tiw.1.A, 3tiw.2.A, 3tm7.1.B, 3tm7.1.D, 4aay.1.A, 4aok.1.B, 4aok.1.D, 4dmr.1.A, 4ga5.1.A, 4ga6.1.A, 4kdi.1.A, 4kdi.2.A, 4kdl.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, 5g4g.1.A, 5glf.1.A, 5glf.2.A, 5glf.3.A, 5glf.4.A, 5ls7.1.L, 5nqd.1.A, 5t5i.1.B, 5t5i.1.D, 5udf.1.A, 5x4l.1.A, 5x4l.2.A, 6btm.1.B, 6cz7.1.A, 6f0k.1.B, 6f49.1.A, 6gcs.1.A, 6hd3.1.A, 6lod.1.B, 6rfq.1.A, 6rfs.1.A, 6s6y.1.B, 6sdr.1.A, 6sdv.1.A, 6tg9.1.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, 7l5i.1.A, 7l5s.1.A, 7q5y.1.A, 7qv7.1.L, 7qv7.1.O, 7t2r.1.A, 7t30.1.A, 7tgh.58.A, 7vw6.1.A, 7w79.1.B, 7w7a.1.B, 7w7a.2.B, 7w7a.2.D, 7w7a.3.D, 7w7d.1.D, 7w7d.3.B, 7wbb.1.A, 7wbb.1.B, 7wbb.1.C, 7wbb.1.D, 7wbb.1.E, 7wbb.1.G, 7z0t.1.G, 7zm7.1.I, 8b9z.1.G, 8ba0.1.G, 8bqg.1.A, 8e73.55.A, 8e9g.1.G