MolNFT v1 · #139716 · protein
Crystal structure of the isochorismatase domain of vabb from vibrio anguillarum 775
5XO1 · Isochorismate lyase: “Crystal structure of the isochorismatase domain of vabb from vibrio anguillarum 775”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #139716 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XO1
- Type
- protein
- Length
- 1,219 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isochorismate lyase
- UniProt
- Q5DK16
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Isochorismate lyase | protein | 203 | 38% helix, 18% strand | Q5DK16 |
| B | Isochorismate lyase | protein | 204 | 37% helix, 18% strand | Q5DK16 |
| D | Isochorismate lyase | protein | 206 | 38% helix, 18% strand | Q5DK16 |
| E | Isochorismate lyase | protein | 205 | 39% helix, 18% strand | Q5DK16 |
| F | Isochorismate lyase | protein | 198 | 37% helix, 20% strand | Q5DK16 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.73 | 0.76 | 92 | empty |
| 2 | 87 | 0.73 | 0.95 | 21 | empty |
| 3 | 113 | 0.73 | 0.93 | 20 | empty |
| 4 | 144 | 0.70 | 0.89 | 23 | empty |
| 5 | 247 | 0.68 | 0.84 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1509 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1488 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1478 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 776 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 720 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5XO1 · Crystal structure of the isochorismatase domain of VabB from Vibrio anguillarum 775 · the same entry in another collection · chain A against A, 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 Q5DK16
- Elsewhere: RCSB PDB 5XO1 · PDBe 5XO1 · UniProt Q5DK16
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