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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
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