3VYU
Crystal structure of the HypC-HypD-HypE complex (form II)
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d3vyua_ | All beta proteins | OB-fold | HupF/HypC-like | HupF/HypC-like | Hydrogenase expression/formation protein HypC | (Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ], | SCOPe (2.08) |
C | d3vyuc1 | Alpha and beta proteins (a+b) | Bacillus chorismate mutase-like | PurM N-terminal domain-like | PurM N-terminal domain-like | Hydrogenase expression/formation protein HypE | (Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ], | SCOPe (2.08) |
C | d3vyuc2 | Alpha and beta proteins (a+b) | PurM C-terminal domain-like | PurM C-terminal domain-like | PurM C-terminal domain-like | Hydrogenase expression/formation protein HypE | (Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | HypC/PAN OB-fold domain-like | 8038052 | 3000354 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | PurM C-terminal domain-like | 8038061 | 3000696 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | PurM N-terminal domain-like | 8038057 | 3001759 | 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 | HupF_HypC | e3vyuA1 | A: beta barrels | X: OB-fold | H: HupF/HypC-like (From Topology) | T: HupF/HypC-like | F: HupF_HypC | ECOD (1.6) |
B | HypD_2nd | e3vyuB3 | A: a/b three-layered sandwiches | X: Hydrogenase expression/formation protein HypD (From Topology) | H: Hydrogenase expression/formation protein HypD (From Topology) | T: Hydrogenase expression/formation protein HypD | F: HypD_2nd | ECOD (1.6) |
B | HypD_1st | e3vyuB1 | A: a/b three-layered sandwiches | X: Hydrogenase expression/formation protein HypD (From Topology) | H: Hydrogenase expression/formation protein HypD (From Topology) | T: Hydrogenase expression/formation protein HypD | F: HypD_1st | ECOD (1.6) |
B | HypD_3rd | e3vyuB2 | A: few secondary structure elements | X: HypD Fe-S cluster binding domain (From Topology) | H: HypD Fe-S cluster binding domain (From Topology) | T: HypD Fe-S cluster binding domain | F: HypD_3rd | ECOD (1.6) |
C | AIRS_C | e3vyuC3 | A: a+b two layers | X: Alpha-beta plaits | H: PurM C-terminal domain-like (From Topology) | T: PurM C-terminal domain-like | F: AIRS_C | ECOD (1.6) |
C | AIRS | e3vyuC4 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: PurM N-terminal domain-like (From Topology) | T: PurM N-terminal domain-like | F: AIRS | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 2.30.30.140 | Mainly Beta | Roll | SH3 type barrels. | CATH (4.3.0) | |
B | 3.40.50.11750 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | HypD, alpha/beta domain 1 | CATH (4.3.0) |
B | 3.40.50.11740 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | HypD, alpha/beta domain 2 | CATH (4.3.0) |
B | 6.10.20.100 | Special | Helix non-globular | Arc Repressor Mutant, subunit A | CATH (4.3.0) | |
C | 3.30.1330.10 | Alpha Beta | 2-Layer Sandwich | 60s Ribosomal Protein L30 | Chain: A | CATH (4.3.0) |
C | 3.90.650.10 | Alpha Beta | Alpha-Beta Complex | Phosphoribosyl-aminoimidazole Synthetase | Chain A, domain 2 | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF01924 | Hydrogenase formation hypA family (HypD) | Hydrogenase formation hypA family | - | Family | |
PF02769 | AIR synthase related protein, C-terminal domain (AIRS_C) | AIR synthase related protein, C-terminal domain | This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of ... | Domain | |
PF00586 | AIR synthase related protein, N-terminal domain (AIRS) | AIR synthase related protein, N-terminal domain | This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase fo ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
Chains | Polymer | Molecular Function | Biological Process | Cellular Component |
---|---|---|---|---|
Hydrogenase expression/formation protein HypC | - | |||
Hydrogenase expression/formation protein HypD | - | |||
Hydrogenase expression/formation protein HypE |
| - |
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR019812 | Hydrogenase assembly chaperone, conserved site | Conserved Site | |
IPR001109 | Hydrogenase expression/formation protein, HupF/HypC | Family | |
IPR002780 | Hydrogenase formation HypD protein | Family | |
IPR042243 | HypD, domain 1 | Homologous Superfamily | |
IPR042244 | HypD, domain 2 | Homologous Superfamily | |
IPR036676 | PurM-like, C-terminal domain superfamily | Homologous Superfamily | |
IPR010918 | PurM-like, C-terminal domain | Domain | |
IPR016188 | PurM-like, N-terminal domain | Domain | |
IPR036921 | PurM-like, N-terminal domain superfamily | Homologous Superfamily | |
IPR011854 | Carbamoyl dehydratase HypE | Family |