MolNFT v1 · #52978 · protein
Crystal structure of the oxa-10 V117T mutant at pH 6.5 inhibited by a chloride ion
2WGV · Beta-lactamase oxa-10: “Crystal structure of the oxa-10 V117T mutant at pH 6.5 inhibited by a chloride ion”. X-ray diffraction, 2 ligands (CL, SO4), 6 pockets (best druggability 0.70). MolNFT v1 #52978 on GenesisL1: 3D structure…
- PDB
- 2WGV
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase oxa-10
- EC
- 3.5.2.6
- UniProt
- P14489
- Ligands
- CL, SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase oxa-10 (EC 3.5.2.6) | protein | 246 | 38% helix, 24% strand | P14489 |
| B | Beta-lactamase oxa-10 (EC 3.5.2.6) | protein | 247 | 38% helix, 24% strand | P14489 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.70 | 0.92 | 31 | GOL |
| 2 | 114 | 0.68 | 0.91 | 32 | GOL |
| 3 | 182 | 0.45 | 0.74 | 32 | SO4 |
| 4 | 55 | 0.34 | 0.77 | 13 | empty |
| 5 | 84 | 0.34 | 0.75 | 15 | CIT |
Interfaces
1 interface between chains.
- A–B · 1432 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2WGV · Crystal structure of the OXA-10 V117T mutant at pH 6.5 inhibited by a chloride ion · the same entry in another collection · chain A against A, TM-score 1.00
- P14489 · AlphaFold monomer V2.0 prediction for beta-lactamase oxa-10 (P14489) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P14489
- Elsewhere: RCSB PDB 2WGV · PDBe 2WGV · UniProt P14489
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