Research workbench
Cdia-ct from uropathogenic escherichia COLI in complex with cognate immunity protein and cysk
Analyse Cdia-ct from uropathogenic escherichia COLI in complex with cognate immunity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J5V
- Type
- protein
- Length
- 1,067 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine synthase a; TRNA nuclease cdia; Immunity protein cdii
- EC
- 2.5.1.47, 3.1.-.-
- UniProt
- P0ABK6, Q0T963, Q0T964
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cysteine synthase a (EC 2.5.1.47) | protein | 313 | 43% helix, 17% strand | P0ABK6 |
| B, E | TRNA nuclease cdia (EC 3.1.-.-) | protein | 96 | 64% helix, 5% strand | Q0T963 |
| C | Immunity protein cdii | protein | 123 | 59% helix, 2% strand | Q0T964 |
| F | Immunity protein cdii | protein | 126 | 56% helix, 2% strand | Q0T964 |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.80 | 0.91 | 54 | empty |
| 2 | 815 | 0.71 | 0.77 | 76 | empty |
| 3 | 795 | 0.70 | 0.76 | 73 | empty |
| 4 | 150 | 0.54 | 0.81 | 27 | empty |
| 5 | 112 | 0.52 | 0.82 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2353 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 1350 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1335 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1088 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1077 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered, cofactor).
Compared structures
- 5J5V · CdiA-CT from uropathogenic Escherichia coli in complex with cognate immunity protein and… · the same entry in another collection · chain F against F, TM-score 1.00
- P0ABK6 · AlphaFold monomer V2.0 prediction for cysteine synthase a (P0ABK6) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q0T964 · AlphaFold monomer V2.0 prediction for immunity protein cdii (Q0T964) · a predicted model of the same protein · chain C against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0ABK6
- Every structure of UniProt Q0T963
- Every structure of UniProt Q0T964
- Elsewhere: RCSB PDB 5J5V · PDBe 5J5V · UniProt P0ABK6 · UniProt Q0T963 · UniProt Q0T964
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