1V74
Structure of the E. coli colicin D bound to its immunity protein ImmD
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d1v74a_ | Alpha and beta proteins (a+b) | Colicin D/E5 nuclease domain | Colicin D/E5 nuclease domain | Colicin D nuclease domain | Colicin D nuclease domain | (Escherichia coli ) [TaxId: 562 ], | SCOPe (2.08) |
B | d1v74b_ | All alpha proteins | Four-helical up-and-down bundle | Colicin D immunity protein | Colicin D immunity protein | Colicin D immunity protein | (Escherichia coli ) [TaxId: 562 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | Colicin D nuclease domain | 8023160 | 4001320 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Colicin D/E5 nuclease domain | 8035540 | 3001283 | SCOP2 (2022-06-29) |
B | SCOP2 Family | Colicin D immunity protein | 8023162 | 4000636 | SCOP2 (2022-06-29) |
B | SCOP2 Superfamily | Colicin D immunity protein | 8035542 | 3000820 | SCOP2 (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 | Colicin_D | e1v74A1 | A: a+b two layers | X: Microbial ribonucleases-like | H: Colicin D nuclease domain (From Topology) | T: Colicin D nuclease domain | F: Colicin_D | ECOD (1.6) |
B | Colicin_immun | e1v74B1 | A: alpha bundles | X: Four-helical up-and-down bundle | H: Colicin D immunity protein (From Topology) | T: Colicin D immunity protein | F: Colicin_immun | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.10.450.200 | Alpha Beta | Roll | Nuclear Transport Factor 2 | Chain: A, | CATH (4.3.0) |
B | 1.20.120.650 | Mainly Alpha | Up-down Bundle | Four Helix Bundle (Hemerythrin (Met), subunit A) | Colicin D | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF11429 | Colicin D (Colicin_D) | Colicin D | Colicin D is a tRNase which kills sensitive E.coli cells via a specific tRNA cleavage. It targets the four isoaccepting tRNAs for Arg and cleaves the phosphodiester bond between positions 38 and 39 at the 3' junction of the anticodon stem and the loo ... | Domain | |
PF09204 | Bacterial self-protective colicin-like immunity (Colicin_immun) | Bacterial self-protective colicin-like immunity | Colicin D, which is synthesised by various prokaryotes, adopts an antiparallel four helical bundle fold: the helices are tightly packed, forming a compact cylindrical molecule. The protein specifically cleaves the anticodon loop of all four tRNA-Arg ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR024440 | Colicin D, C-terminal | Domain | |
IPR024575 | Cloacin/colicin | Family | |
IPR038233 | Colicin D/E5 nuclease domain superfamily | Homologous Superfamily | |
IPR016128 | Pyosin/cloacin translocation domain | Domain | |
IPR036302 | Pyosin/cloacin translocation domain superfamily | Homologous Superfamily | |
IPR037178 | Colicin D, C-terminal domain superfamily | Homologous Superfamily | |
IPR015287 | Colicin D immunity protein domain | Domain | |
IPR036471 | Colicin D superfamily | Homologous Superfamily |