Research workbench
Crystal structure of uncharacterized metallo protein from vibrio cholerae with beta-lactamase like fold
Analyse Crystal structure of uncharacterized metallo protein from vibrio cholerae with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BV6
- Type
- protein
- Length
- 2,122 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal-dependent hydrolase
- UniProt
- A6A5N8
- Ligands
- FE
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Metal-dependent hydrolase | protein | 353 | 28% helix, 22% strand | A6A5N8 |
| B, D, E, F | Metal-dependent hydrolase | protein | 354 | 29% helix, 21% strand | A6A5N8 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.86 | 0.88 | 51 | empty |
| 2 | 907 | 0.86 | 0.88 | 53 | empty |
| 3 | 959 | 0.85 | 0.87 | 52 | empty |
| 4 | 143 | 0.81 | 0.98 | 25 | empty |
| 5 | 140 | 0.81 | 0.98 | 25 | empty |
Interfaces
15 interfaces between chains.
- D–E · 4937 Ų buried · 76 hydrogen bonds · protein-protein
- A–F · 4892 Ų buried · 75 hydrogen bonds · protein-protein
- B–C · 4885 Ų buried · 81 hydrogen bonds · protein-protein
- C–D · 1528 Ų buried · 50 hydrogen bonds · protein-protein
- E–F · 1524 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 3BV6 · Crystal structure of uncharacterized metallo protein from Vibrio cholerae with… · 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 A6A5N8
- Elsewhere: RCSB PDB 3BV6 · PDBe 3BV6 · UniProt A6A5N8
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