|  | SWISS-MODEL Homology Modelling Report

## Model Building Report

This document lists the results for the homology modelling project "21_Jan_SF_Bin67_scaffold_32672_c1:3-2330_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 282 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 | 0.81 | 0.78 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 53.57 | monomer | 0.00 | HHblits | X-ray | 2.97Å | 0.46 | 1 - 772 | 1.00 | 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    RPFLERFTDMPLLVRLDTLQRLRADEVFADYSSDLDVDGPSFTLHGMTEEQHERNGDRVVFDDASGALRAINREDVGDRL
    7b04.1.B  ADYVKKFTDFPLLIRTDTLKRVSPKDIIPNYKLQDISDGPSYHIQGLKDEQREIIGDFVVWDAKSKGPKAITRDDVGETL

    Target    DDKGIDPALDYQGTVTLVDGSTVEVMSVLSMYREHLADYDIDSVVDMTGAPRNLIEQLLDDMTTLSPVAFHVGEGVNHYF
    7b04.1.B  VKKGIDPVLEGSFKLKTIDGKEIEVMTLLEMYKIHLRDYDIDSVVSMTNSPKDLIERLAKDIATIKPVAIHYGEGVNHYF

    Target    HATLHNRATYLVGMLLGSVGVSGGGVSTWAGNYKGGVFQAAPWFGPGVGGFVNEDPFHPLTDPSARYSAETARHLVHGED
    7b04.1.B  HATLMNRSYYLPVMLTGNVGYFGSGSHTWAGNYKAGNFQASKWSGPGFYGWVAEDVFKPNLDPYASAKDLNIKGRALDEE

    Target    TSYWGFGDRPLVVDTPEDGRKVFTGTTHMPTPTKALWYNNANLINQAKWHYELVKNVNPKVDLIVDQQIEWTGSAEFADI
    7b04.1.B  VAYWNHSERPLIVNTPKYGRKVFTGKTHMPSPTKVLWFTNVNLINNAKHVYQMLKNVNPNIEQIMSTDIEITGSIEYADF

    Target    VLPANSWMEAETWEMGASCSNPFLQVWK-GGIEPLNDTRDDIAIFAGVANALTELTGDERFSQAFMF--ADRPEVYLDRV
    7b04.1.B  AFPANSWVEFQEFEITNSCSNPFIQIWGKTGITPVYESKDDVKILAGMASKLGELLRDKRFEDNWKFAIEGRASVYINRL

    Target    LAGSFTTEGYTVEDLTAGRYGPPGGALMQYRSYPRIPFKEQIEDSLPFYTDTGRMHGYVDIPEAIEYGENLIVHREAVEA
    7b04.1.B  LDGSTTMKGYTCEDILNGKYGEPGVAMLLFRTYPRHPFWEQVHESLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGPEA

    Target    TPYLPNVIVSTSPYLRPRDYGIAPEELDGDARSVRNIMMSWAEVKETENPLFAAGYNYLCLTPKSRHAVHSSWAVTDWHW
    7b04.1.B  TPYLPNAIVSTNPYIRPDDYGIPENAEYWEDRTVRNIKKSWEETKKTKNFLWEKGYHFYCVTPKSRHTVHSQWAVTDWNF

    Target    LWSSSFSDPYRVETRAPGVGEPAIHLNPDDARSLGIRNGDYVWVDSNPKDRPYRDADVDESFLDVARLLVRVTYNPAYPP
    7b04.1.B  IWNNNFGDPYRMDKRMPGVGEHQIHIHPQAARDLGIEDGDYVYVDANPADRPYEGWKPNDSFYKVSRLMLRAKYNPAYPY

    Target    GVTMLKHAFYMATPRTFRAAQERSDGRALAETTGYQSSFRSGSHQSITRGWAPPMHQTDSLFHKRAGVFGFTYGFDVDNH
    7b04.1.B  NCTMMKHSAWISSDKTVQAHETRPDGRALSP-SGYQSSFRYGSQQSITRDWSMPMHQLDSLFHKAKIGMKFIFGFEADNH

    Target    AINTVPKETVVRITKAEDGGVGGSGAWTRGRPGSMPGDEDDAMQAYLAGELTVVRRT
    7b04.1.B  CINTVPKETLVKITKAENGGMGGKGVWDPVKTGYTAGNENDFMKKFLNGELIKVD--

### Model #02 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.40 | 0.45 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
3ir7.1.A | 22.74 | monomer | 0.00 | HHblits | X-ray | 2.50Å | 0.31 | 1 - 739 | 0.80 | 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    RPFLERFTDMPLLVRLD-------TLQRLRADEVFADYSSDLDVDGPSFTLHGMTEEQHERNGDRVVFDDASGALRAINR
    3ir7.1.A  TDYVRRYTDMPMLVMLEERDGYYAAGRMLRAADLVDAL-------GQ----------ENNPEWKTVAFNT-NGEMVAPNG

    Target    EDVGD--------------------RLD---DK------------------------GIDPALDY---QGTVTLVDGSTV
    3ir7.1.A  SIGFRWGEKGKWNLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTA

    Target    EVMSVLSMYR------------------EHLADYDIDSVVDMTGAPRNLIEQLLDDMTTL-----SPVAFHVGEGVNHYF
    3ir7.1.A  LVTTVYDLTLANYGLERGLNDVNCATSYDDVKAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWY

    Target    HATLHNRATYLVGMLLGSVGVSGGGVSTWAGNYKGGV---FQ----AAPWFGPGVGGFVNEDPFHPLTDPSARYSA----
    3ir7.1.A  HLDMNYRGLINMLIFCGCVGQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQRPA--RHMNSTSYFYNHSSQWRYETVTAE

    Target    --------------ETAR----HLVHGEDTSYWGFGDRPL----------------VVDTPEDGRKVF--TGTTHMPTPT
    3ir7.1.A  ELLSPMADKSRYTGHLIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHP

    Target    KALWYNNANLINQAKWHYEL-------------------------------VKNVNPKVDLIVDQQIEWTGSAEFADIVL
    3ir7.1.A  RNLFIWRSNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIIL

    Target    PANSWMEAETWEMGASCSNPFLQVWKGGIEPLNDTRDDIAIFAGVANALTELTGDE---R---FSQAFMFADRP------
    3ir7.1.A  PTATWYEKDDMN--TSDMHPFIHPLSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPI-QHDSAAELAQP

    Target    ---EVY---------------------------------------------------------LDRV-------------
    3ir7.1.A  LDVKDWKKGECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQP

    Target    ------------LAGSFTTEG----YTVEDLTAGRYG-----PP--GGALMQYR---------------------SYPRI
    3ir7.1.A  MLNTAIDAAEMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYN

    Target    PFKEQIEDSLPFYTDTGRMHGYVDIPEAIEYGENLIVHREAVEATPYLPNVIVSTSPYLRPRDYGIAPEELDGDARSVRN
    3ir7.1.A  AGYTNVHELIPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSV-KE------------------------------

    Target    IMMSWAEVKETENPLFAAGYNYLCLTPKSRHAVHSSWAVTDWHWLWSSSFSDPYRVETRAPGVGEPAIHLNPDDARSLGI
    3ir7.1.A  ----VI---G-QKSNGNQEKALNFLTPHQKWGIHSTYSDNLLM------------LTL---GRGGPVVWLSEADAKDLGI

    Target    RNGDYVWVDSNPKDRPYRDADVDESFLDVARLLVRVTYNPAYPPGVTMLKHAFYMATPRTFRAAQERSDGRALAETTGYQ
    3ir7.1.A  ADNDWIEVFNS-----------------NGALTARAVVSQRVPAGMTMMYHAQERIVN------------LPGSEI----

    Target    SSFRSGSHQSITRGWAPPMHQTDSLFHKRAGVFGFTYGFDVDNHAINTVPKETVVRITKAEDGGVGGSGAWTRGRPGSMP
    3ir7.1.A  TQQRGGIHNSVTRITPKPTHMI-------GGYAHLAYGFNYYGT--VGSNRDEFVVVRKMKNIDWL--------------

    Target    GDEDDAMQAYLAGELTVVRRT
    3ir7.1.A  ---------------------

### Model #03 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.21 | 0.37 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
2ivf.1.A | 32.76 | monomer | 0.00 | BLAST | X-ray | 1.88Å | 0.36 | 1 - 473 | 0.53 | 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    RPFLERFTDMPLLVRLDTLQRLRADEVFADYSSDLDVDGPSFTLHGMTEEQHERNGDRVVFDDASGALRAINREDVGDRL
    2ivf.1.A  RQFVCEQTDLPLLVRMDTGKFLSAE----------DVDG------GEAKQFY-------FFDEKAGSVRKASRGTL--KL

    Target    DDKGIDPALDYQGTVTLVDGSTVEVMSVLSMYREHLADYDIDSVVDMTGAPRNLIEQLLDDMTTLSPVAFHVGEGVNHYF
    2ivf.1.A  D---FMPALEGTFSARLKNGKTIQVRTVFEGLREHLKDYTPEKASAKCGVPVSLIRELGRKVAKKRTCSY-IGFSSAKSY

    Target    HATLHNRATYLVGMLLGSVGVSGGGVSTWAGNYKGGVFQAAPWFGPGVGGFV------NEDPFHPLTDPSARYSAETARH
    2ivf.1.A  HGDLMERSLFLAMAL--------------SGN----------WGKPGTGAFAWAYSDDNMVYLGVMSKPTAQGGMDELHQ

    Target    LVHGEDTSYWGFGDRPLVVD---TPEDGR----KVFTGTTHMPTPTKALWYNNA--NLINQAKW----------------
    2ivf.1.A  MAE-------GFNKRTLEADPTSTDEMGNIEFMKVVTSAVGLVPPAMWLYYHVGYDQLWNNKAWTDPALKKSFGAYLDEA

    Target    ---------HYELVKNVNPKVDLIVDQ---------------------------QIEWTGSAEFADIVLPANSWMEAETW
    2ivf.1.A  KEKGWWTNDHIRPAPDKTPQVYMLLSQNPMRRKRSGAKMFPDVLFPKLKMIFALETRMSSSAMYADIVLPCAWYYEKH--

    Target    EMGASCS-NPFLQVWKGGIEPLNDTR---DDIAIFA------GVANALTELTG--------DERFSQAFMFAD-------
    2ivf.1.A  EMTTPCSGNPFFTFVDRSVAPPGECREEWDAIALILKKVGERAAARGLTEFNDHNGRKRRYDELYKKFTMDGHLLTNEDC

    Target    -RPEVYLDR---VLAGSFTTEGYTVEDLTAGRYGPPGGALMQYR-------SYPRIPFKEQIEDSLPFYTDTGRMHGYVD
    2ivf.1.A  LKEMVDINRAVGVFAKDYTYEKFKKEGQT--RFLSMGTGVSRYAHANEVDVTKPIYPMRWHFDDKKVFPTHTRRAQFYLD

    Target    IPEAIEYGENLIVHREAVEATPYLPNVIVSTSPYLRPRDYGIAPEELDGDARSVRNIMMSWAEVKETENPLFAAGYNYLC
    2ivf.1.A  HDWYLEAGESLPTHKD----------------------------------------------------------------

    Target    LTPKSRHAVHSSWAVTDWHWLWSSSFSDPYRVETRAPGVGEPAIHLNPDDARSLGIRNGDYVWVDSNPKDRPYRDADVDE
    2ivf.1.A  --------------------------------------------------------------------------------

    Target    SFLDVARLLVRVTYNPAYPPGVTMLKHAFYMATPRTFRAAQERSDGRALAETTGYQSSFRSGSHQSITRGWAPPMHQTDS
    2ivf.1.A  --------------------------------------------------------------------------------

    Target    LFHKRAGVFGFTYGFDVDNHAINTVPKETVVRITKAEDGGVGGSGAWTRGRPGSMPGDEDDAMQAYLAGELTVVRRT
    2ivf.1.A  -----------------------------------------------------------------------------

### Model #04 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.12 | 0.33 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
2fug.2.C | 16.58 | monomer | 0.00 | HHblits | X-ray | 3.30Å | 0.27 | 296 - 649 | 0.25 | 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    RPFLERFTDMPLLVRLDTLQRLRADEVFADYSSDLDVDGPSFTLHGMTEEQHERNGDRVVFDDASGALRAINREDVGDRL
    2fug.2.C  --------------------------------------------------------------------------------

    Target    DDKGIDPALDYQGTVTLVDGSTVEVMSVLSMYREHLADYDIDSVVDMTGAPRNLIEQLLDDMTTLSPVAFHVGEGVNHYF
    2fug.2.C  --------------------------------------------------------------------------------

    Target    HATLHNRATYLVGMLLGSVGVSGGGVSTWAGNYKGGVFQAAPWFGPGVGGFVNEDPFHPLTDPSARYSAETARHLVHGED
    2fug.2.C  --------------------------------------------------------------------------------

    Target    TSYWGFGDRPLVVDTPEDGRKVFTGTTHMPTPTKALWYNNANLINQAKWHYELVKNVNPKVDLIVDQQIEWTGSA-EFAD
    2fug.2.C  -------------------------------------------------------EALKGKRFVVMHLSHLHPLAERYAH

    Target    IVLPANSWMEAETWEMGASCSNPFLQVWKGGIEPLNDTRDDIAIFAGVANALTELTGDERFSQAFMFADRPEVYLDRVLA
    2fug.2.C  VVLPAPTFYEKRGH---LVNLEGRVLPLSPAPIENGEAEGALQVLALLAEALGVR-------P--PFR-LHLEA------

    Target    GSFTTEGYTVEDLTAGRYGPPGGALMQYRSYPRIPFKEQIEDSLPFYTDTGRMHGYVDIPEAIEYGENLIVHREAVEATP
    2fug.2.C  ---------QKALKA----------------------------RKVPEAMGRLSFRLKELR------------------P

    Target    YLPNVIVSTSPYLRPRDYGIAPEELDGDARSVRNIMMSWAEVKETENPLFAAGYNYLCLTPKSRHAVHSSWAVTDWHWLW
    2fug.2.C  -------------------------------------------------KERKGAFYLRPTMW--KAHQ---AVGK--A-

    Target    SSSFSDPYRVETRAPGVGEPAIHLNPDDARSLGIRNGDYVWVDSNPKDRPYRDADVDESFLDVARLLVRVTYNPAYPPGV
    2fug.2.C  ---------Q-----EAARAELWAHPETARAEALPEGAQVAVETP-----------------FGRVEARVVHREDVPKGH

    Target    TMLKHAFYMATPRTFRAAQERSDGRALAETTGYQSSFRSGSHQSITRGWAPPMHQTDSLFHKRAGVFGFTYGFDVDNHAI
    2fug.2.C  LYLSALGPAAG---------------------------------------------------------------------

    Target    NTVPKETVVRITKAEDGGVGGSGAWTRGRPGSMPGDEDDAMQAYLAGELTVVRRT
    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.

RPFLERFTDMPLLVRLDTLQRLRADEVFADYSSDLDVDGPSFTLHGMTEEQHERNGDRVVFDDASGALRAINREDVGDRLDDKGIDPALDYQGTVTLVDG
STVEVMSVLSMYREHLADYDIDSVVDMTGAPRNLIEQLLDDMTTLSPVAFHVGEGVNHYFHATLHNRATYLVGMLLGSVGVSGGGVSTWAGNYKGGVFQA
APWFGPGVGGFVNEDPFHPLTDPSARYSAETARHLVHGEDTSYWGFGDRPLVVDTPEDGRKVFTGTTHMPTPTKALWYNNANLINQAKWHYELVKNVNPK
VDLIVDQQIEWTGSAEFADIVLPANSWMEAETWEMGASCSNPFLQVWKGGIEPLNDTRDDIAIFAGVANALTELTGDERFSQAFMFADRPEVYLDRVLAG
SFTTEGYTVEDLTAGRYGPPGGALMQYRSYPRIPFKEQIEDSLPFYTDTGRMHGYVDIPEAIEYGENLIVHREAVEATPYLPNVIVSTSPYLRPRDYGIA
PEELDGDARSVRNIMMSWAEVKETENPLFAAGYNYLCLTPKSRHAVHSSWAVTDWHWLWSSSFSDPYRVETRAPGVGEPAIHLNPDDARSLGIRNGDYVW
VDSNPKDRPYRDADVDESFLDVARLLVRVTYNPAYPPGVTMLKHAFYMATPRTFRAAQERSDGRALAETTGYQSSFRSGSHQSITRGWAPPMHQTDSLFH
KRAGVFGFTYGFDVDNHAINTVPKETVVRITKAEDGGVGGSGAWTRGRPGSMPGDEDDAMQAYLAGELTVVRRT

## Table T2:

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 53.57 | monomer | - | HHblits | X-ray | 2.97Å | 0.46 | 1.00 | Nitrite oxidoreductase subunit A
7b04.1.B | 54.04 | monomer | - | BLAST | X-ray | 2.97Å | 0.46 | 0.99 | Nitrite oxidoreductase subunit A
7b04.2.B | 53.57 | monomer | - | HHblits | X-ray | 2.97Å | 0.46 | 1.00 | Nitrite oxidoreductase subunit A
7b04.2.B | 54.04 | monomer | - | BLAST | X-ray | 2.97Å | 0.46 | 0.99 | Nitrite oxidoreductase subunit A
3ir7.1.A | 22.74 | monomer | - | HHblits | X-ray | 2.50Å | 0.31 | 0.80 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 22.85 | homo-dimer | 0.06 | HHblits | X-ray | 1.90Å | 0.31 | 0.80 | Respiratory nitrate reductase 1 alpha chain
3ir6.1.A | 23.05 | monomer | - | HHblits | X-ray | 2.80Å | 0.32 | 0.80 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 22.74 | monomer | - | HHblits | X-ray | 1.90Å | 0.31 | 0.80 | Respiratory nitrate reductase 1 alpha chain
3ir5.1.A | 22.58 | monomer | - | HHblits | X-ray | 2.30Å | 0.31 | 0.80 | Respiratory nitrate reductase 1 alpha chain
1r27.4.A | 22.74 | homo-dimer | - | HHblits | X-ray | 2.00Å | 0.31 | 0.80 | Respiratory nitrate reductase 1 alpha chain
1dms.1.A | 21.85 | monomer | - | HHblits | X-ray | 1.88Å | 0.30 | 0.57 | DMSO REDUCTASE
1e60.1.A | 21.95 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.57 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e5v.2.A | 21.95 | monomer | - | HHblits | X-ray | 2.40Å | 0.30 | 0.57 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e18.1.A | 22.12 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.57 | DMSO REDUCTASE.
4dmr.1.A | 21.80 | monomer | - | HHblits | X-ray | 1.90Å | 0.30 | 0.57 | DMSO REDUCTASE
2ivf.1.A | 32.76 | monomer | - | BLAST | X-ray | 1.88Å | 0.36 | 0.53 | ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
6q8o.1.C | 16.58 | monomer | - | HHblits | X-ray | 3.61Å | 0.27 | 0.25 | NADH-quinone oxidoreductase subunit 3
6zjl.1.C | 16.58 | monomer | - | HHblits | EM | NA | 0.27 | 0.25 | NADH-quinone oxidoreductase subunit 3
6ziy.1.C | 16.58 | monomer | - | HHblits | EM | NA | 0.27 | 0.25 | NADH-quinone oxidoreductase subunit 3
6zjn.1.C | 16.58 | monomer | - | HHblits | EM | NA | 0.27 | 0.25 | NADH-quinone oxidoreductase subunit 3
3m9s.1.C | 16.58 | monomer | - | HHblits | X-ray | 4.50Å | 0.27 | 0.25 | NADH-quinone oxidoreductase subunit 3
6zjy.1.C | 16.58 | monomer | - | HHblits | EM | NA | 0.27 | 0.25 | NADH-quinone oxidoreductase subunit 3
2fug.2.C | 16.58 | monomer | - | HHblits | X-ray | 3.30Å | 0.27 | 0.25 | NADH-quinone oxidoreductase chain 3
6zk9.1.C | 16.18 | monomer | - | HHblits | EM | NA | 0.27 | 0.22 | NADH:ubiquinone oxidoreductase core subunit S1
7zd6.1.4 | 16.18 | monomer | - | HHblits | EM | NA | 0.27 | 0.22 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7dgr.10.A | 16.18 | monomer | - | HHblits | EM | NA | 0.27 | 0.22 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6qcf.1.C | 15.61 | monomer | - | HHblits | EM | NA | 0.27 | 0.22 | NADH:ubiquinone oxidoreductase core subunit S1
6qc5.1.C | 15.61 | monomer | - | HHblits | EM | NA | 0.27 | 0.22 | NADH:ubiquinone oxidoreductase core subunit S1
5o31.1.8 | 16.18 | monomer | - | HHblits | EM | 4.13Å | 0.27 | 0.22 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
2pjh.1.B | 11.54 | monomer | - | HHblits | NMR | NA | 0.26 | 0.07 | Transitional endoplasmic reticulum ATPase
5x4l.2.A | 11.32 | monomer | - | HHblits | X-ray | 2.40Å | 0.26 | 0.07 | Transitional endoplasmic reticulum ATPase
3ir5.1.A | 12.96 | monomer | - | HHblits | X-ray | 2.30Å | 0.25 | 0.07 | Respiratory nitrate reductase 1 alpha chain
5x4l.1.A | 11.32 | monomer | - | HHblits | X-ray | 2.40Å | 0.26 | 0.07 | Transitional endoplasmic reticulum ATPase
4kdl.1.A | 11.54 | monomer | - | HHblits | X-ray | 1.81Å | 0.26 | 0.07 | Transitional endoplasmic reticulum ATPase
5b6c.1.A | 11.54 | monomer | - | HHblits | X-ray | 1.55Å | 0.26 | 0.07 | Transitional endoplasmic reticulum ATPase
3qc8.1.A | 11.76 | monomer | - | HHblits | X-ray | 2.20Å | 0.26 | 0.07 | Transitional endoplasmic reticulum ATPase
4kdi.1.A | 11.54 | monomer | - | HHblits | X-ray | 1.86Å | 0.26 | 0.07 | Transitional endoplasmic reticulum ATPase
3ir6.1.A | 12.96 | monomer | - | HHblits | X-ray | 2.80Å | 0.25 | 0.07 | Respiratory nitrate reductase 1 alpha chain
4kdi.2.A | 11.54 | monomer | - | HHblits | X-ray | 1.86Å | 0.26 | 0.07 | Transitional endoplasmic reticulum ATPase
1r27.4.A | 12.96 | monomer | - | HHblits | X-ray | 2.00Å | 0.25 | 0.07 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 13.21 | monomer | - | HHblits | X-ray | 2.50Å | 0.25 | 0.07 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 12.96 | monomer | - | HHblits | X-ray | 1.90Å | 0.25 | 0.07 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 12.96 | monomer | - | HHblits | X-ray | 1.90Å | 0.25 | 0.07 | Respiratory nitrate reductase 1 alpha chain
1e60.1.A | 14.55 | monomer | - | HHblits | X-ray | 2.00Å | 0.27 | 0.07 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e18.1.A | 14.55 | monomer | - | HHblits | X-ray | 2.00Å | 0.27 | 0.07 | DMSO REDUCTASE.
1e5v.2.A | 14.55 | monomer | - | HHblits | X-ray | 2.40Å | 0.27 | 0.07 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
4dmr.1.A | 14.81 | monomer | - | HHblits | X-ray | 1.90Å | 0.27 | 0.07 | DMSO REDUCTASE
1dms.1.A | 14.81 | monomer | - | HHblits | X-ray | 1.88Å | 0.27 | 0.07 | DMSO REDUCTASE
5cup.1.A | 46.15 | monomer | - | HHblits | X-ray | 2.10Å | 0.43 | 0.03 | Phosphate propanoyltransferase
5cuo.1.A | 46.15 | monomer | - | HHblits | X-ray | 1.54Å | 0.43 | 0.03 | Phosphate propanoyltransferase

The table above shows the top 50 filtered templates. A further 179 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, 1eu1.1.A, 1fdo.1.A, 1g8j.1.A, 1g8k.1.A, 1h0h.1.A, 1j75.1.A, 1kqf.1.A, 1ogy.1.A, 1tmo.1.A, 1uhd.1.B, 1uhe.1.B, 1wlf.1.A, 2d9r.1.A, 2e7z.1.A, 2heo.1.A, 2heo.1.B, 2iv2.1.A, 2ivf.1.A, 2ki8.1.A, 2kz3.1.A, 2l1p.1.A, 2lnb.1.A, 2mrn.1.A, 2mru.1.A, 2mru.1.B, 2nya.1.A, 2o3f.1.A, 2v3v.1.A, 2v45.1.A, 2vpx.1.D, 2vpz.1.A, 2xvc.1.A, 3hu1.1.A, 3hu2.1.A, 3iwf.1.A, 3nzl.1.A, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3plx.1.B, 3qq7.1.A, 3qq8.1.A, 3qwz.1.A, 3tiw.1.A, 3tiw.2.A, 4aay.1.A, 4ga5.1.A, 4ga6.1.A, 4rv0.1.A, 4v4c.1.A, 4ydd.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, 5gpn.24.A, 5itm.1.A, 5itm.1.B, 5itm.1.E, 5nqd.1.A, 5t5i.1.B, 5t5i.1.D, 5xtb.1.L, 6btm.1.B, 6cz7.1.A, 6f0k.1.B, 6f49.1.A, 6g72.1.G, 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, 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.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, 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, 7ur8.1.A, 7v2c.1.L, 7vw6.1.A, 7vxu.1.L, 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