Research workbench
Structure of the ai-2 exporter family protein ydik from E. COLI
Analyse Structure of the ai-2 exporter family protein ydik from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OT9
- Type
- protein
- Length
- 1,105 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ai-2E member ydik
- UniProt
- P0AFS7
- Pockets
- 13 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, D, C, B | Ai-2E member ydik | protein | 221 | 77% helix, 0% strand | P0AFS7 |
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.81 | 0.81 | 80 | empty |
| 2 | 991 | 0.81 | 0.81 | 79 | empty |
| 3 | 1030 | 0.81 | 0.81 | 80 | empty |
| 4 | 613 | 0.77 | 0.82 | 52 | empty |
| 5 | 600 | 0.77 | 0.82 | 53 | empty |
Interfaces
10 interfaces between chains.
- D–C · 1439 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 1434 Ų buried · 10 hydrogen bonds · protein-protein
- E–D · 1432 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1428 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 1417 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7OT9 · Structure of the AI-2 exporter family protein YdiK from E. coli · the same entry in another collection · chain C against C, TM-score 1.00
- P0AFS7 · AlphaFold monomer V2.0 prediction for putative transport protein ydik (P0AFS7) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 P0AFS7
- Elsewhere: RCSB PDB 7OT9 · PDBe 7OT9 · UniProt P0AFS7
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