MolNFT v1 · #13156 · protein
Crystal structure of the yersinia virulence effector yope chaperone-binding domain in complex with its secretion chaperone, syce
1L2W · Yope regulator: “Crystal structure of the yersinia virulence effector yope chaperone-binding domain in complex with its…”. X-ray diffraction, 15 pockets (best druggability 0.83). MolNFT v1 #13156 on GenesisL1: 3D structure, binding…
- PDB
- 1L2W
- Type
- protein
- Length
- 1,172 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yope regulator; Outer membrane virulence protein yope
- UniProt
- P08008
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yope regulator | protein | 122 | 30% helix, 26% strand | — |
| B, C, E, H | Yope regulator | protein | 117 | 30% helix, 28% strand | — |
| D | Yope regulator | protein | 121 | 31% helix, 27% strand | — |
| F, G | Yope regulator | protein | 119 | 29% helix, 27% strand | — |
| I | Outer membrane virulence protein yope | protein | 57 | 30% helix, 19% strand | P08008 |
| J | Outer membrane virulence protein yope | protein | 56 | 30% helix, 21% strand | P08008 |
| K, L | Outer membrane virulence protein yope | protein | 55 | 31% helix, 20% strand | P08008 |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.83 | 0.84 | 104 | empty |
| 2 | 115 | 0.73 | 0.94 | 20 | empty |
| 3 | 139 | 0.72 | 0.92 | 29 | empty |
| 4 | 163 | 0.67 | 0.87 | 28 | empty |
| 5 | 657 | 0.66 | 0.75 | 65 | empty |
Interfaces
21 interfaces between chains.
- E–F · 1413 Ų buried · 14 hydrogen bonds · protein-protein
- C–J · 1404 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1402 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1400 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1391 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1L2W · Crystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in… · the same entry in another collection · chain L against L, TM-score 1.00
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 P08008
- Elsewhere: RCSB PDB 1L2W · PDBe 1L2W · UniProt P08008
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