Research workbench
Crystal structure of the isochorismatase domain of VabB from Vibrio anguillarum 775
Analyse Crystal structure of the isochorismatase domain of VabB from Vibrio anguillarum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XO1
- Type
- protein
- Length
- 1,219 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.23
- Source
- Vibrio anguillarum 775
- Molecule
- Isochorismate lyase
- UniProt
- Q5DK16
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.23 · 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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