Research workbench
The crystal structure of vabb-icl domain from vibrio anguillarum 775
Analyse The crystal structure of vabb-icl domain from vibrio anguillarum 775 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WXV
- Type
- protein
- Length
- 2,376 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isochorismate lyase
- UniProt
- Q5DK16
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Isochorismate lyase | protein | 198 | 38% helix, 18% strand | Q5DK16 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.79 | 0.80 | 98 | empty |
| 2 | 1025 | 0.73 | 0.77 | 80 | empty |
| 3 | 946 | 0.73 | 0.77 | 77 | empty |
| 4 | 136 | 0.69 | 0.89 | 23 | empty |
| 5 | 132 | 0.68 | 0.89 | 21 | empty |
Interfaces
15 interfaces between chains.
- I–J · 1496 Ų buried · 19 hydrogen bonds · protein-protein
- B–K · 1493 Ų buried · 19 hydrogen bonds · protein-protein
- E–L · 1480 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 1466 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1464 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5WXV · The crystal structure of VabB-ICL domain 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 5WXV · PDBe 5WXV · UniProt Q5DK16
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