1Y5I
The crystal structure of the NarGHI mutant NarI-K86A
External Resource: Annotation
- Domain Annotation: SCOP/SCOPe Classification
- Domain Annotation: SCOP2 Classification
- Domain Annotation: ECOD Classification
- Domain Annotation: CATH
- Protein Family Annotation
- Gene Ontology: Gene Product Annotation
- InterPro: Protein Family Classification
- Membrane Protein Annotation: PDBTM
- Membrane Protein Annotation: MemProtMD
- Membrane Protein Annotation: mpstruc
- Protein Modification Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8021728 | 4000801 | SCOP2 (2022-06-29) |
A | SCOP2 Family | Formate dehydrogenase/DMSO reductase, C-terminal domain | 8021729 | 4002360 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Formate dehydrogenase/DMSO reductase, domains 1-3 | 8034108 | 3001453 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | ADC-like | 8034109 | 3001132 | SCOP2 (2022-06-29) |
B | SCOP2 Family | Ferredoxin domains from multidomain proteins | 8021730 | 4000021 | SCOP2 (2022-06-29) |
B | SCOP2 Superfamily | 4Fe-4S ferredoxins | 8034110 | 3000020 | SCOP2 (2022-06-29) |
C | SCOP2B Superfamily | Respiratory nitrate reductase 1 gamma chain | 8039525 | 3000332 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | Molydop_binding | e1y5iA1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: Molydop_binding | ECOD (1.6) |
A | NarG | e1y5iA3 | A: a+b two layers | X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology) | H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domain 1 | F: NarG | ECOD (1.6) |
A | Molybdopterin_2nd | e1y5iA4 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domains 2 and 3 | F: Molybdopterin_2nd | ECOD (1.6) |
A | Molybdopterin_1st_1 | e1y5iA5 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domains 2 and 3 | F: Molybdopterin_1st_1 | ECOD (1.6) |
B | Fer4_11 | e1y5iB3 | A: a+b two layers | X: 4Fe-4S ferredoxin (From Topology) | H: 4Fe-4S ferredoxin (From Topology) | T: 4Fe-4S ferredoxin | F: Fer4_11 | ECOD (1.6) |
B | Nitr_red_bet_C_1 | e1y5iB2 | A: a+b two layers | X: 4Fe-4S ferredoxin (From Topology) | H: 4Fe-4S ferredoxin (From Topology) | T: 4Fe-4S ferredoxin | F: Nitr_red_bet_C_1 | ECOD (1.6) |
C | Nitrate_red_gam | e1y5iC1 | A: alpha bundles | X: Transmembrane heme-binding four-helical bundle (From Homology) | H: Transmembrane heme-binding four-helical bundle | T: Respiratory nitrate reductase 1 gamma chain | F: Nitrate_red_gam | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.40.50.12770 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Nitrate reductase alpha subunit | CATH (4.3.0) |
A | 2.40.40.20 | Mainly Beta | Beta Barrel | Barwin-like endoglucanases | CATH (4.3.0) | |
B | 3.30.70.20 | Alpha Beta | 2-Layer Sandwich | Alpha-Beta Plaits | CATH (4.3.0) | |
B | 1.10.3650.10 | Mainly Alpha | Orthogonal Bundle | nitrate reductase domain fold | nitrate reductase domain like | CATH (4.3.0) |
C | 1.20.950.20 | Mainly Alpha | Up-down Bundle | Fumarate Reductase Cytochrome B subunit | Transmembrane di-heme cytochromes, Chain C | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF01568 | Molydopterin dinucleotide binding domain (Molydop_binding) | Molydopterin dinucleotide binding domain | This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entir ... | Domain | |
PF00384 | Molybdopterin oxidoreductase (Molybdopterin) | Molybdopterin oxidoreductase | - | Family | |
PF14710 | Respiratory nitrate reductase alpha N-terminal (Nitr_red_alph_N) | Respiratory nitrate reductase alpha N-terminal | This is the N-terminal tail of the respiratory nitrate reductase alpha chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. The N-terminal tail of the alpha chain interacts with the beta ... | Domain | |
PF13247 | 4Fe-4S dicluster domain (Fer4_11) | 4Fe-4S dicluster domain | Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ... | Domain | |
PF14711 | Respiratory nitrate reductase beta C-terminal (Nitr_red_bet_C) | Respiratory nitrate reductase beta C-terminal | This domain occurs near the C-terminus of the respiratory nitrate reductase beta chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. This domain plays a role in the interactions between ... | Domain | |
PF02665 | Nitrate reductase gamma subunit (Nitrate_red_gam) | Nitrate reductase gamma subunit | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Membrane Protein Annotation: PDBTM PDBTM Database Homepage
Chains | External Link | Comment |
---|---|---|
PDBTM | Annotated as membrane protein by PDBTM |
Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage
Chains | External Link | Comment |
---|---|---|
MemProtMD | Annotated as membrane protein by MemProtMD |
Membrane Protein Annotation: mpstruc mpstruc Database Homepage
Chains | Resource Link | Group | Subgroup | Protein |
---|---|---|---|---|
mpstruc | TRANSMEMBRANE PROTEINS: ALPHA-HELICAL | Oxidoreductases | NarGHI Nitrate Reductase with pentachlorophenol (PCP) |
Protein Modification Annotation
Modified Residue(s) | ||
---|---|---|
Chain | Residue(s) | Description |
FME | Parent Component: MET :  AA0021 , AA0566 :  N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 |