Research workbench
Crystal structure of the acyl-enzyme oxa-10 W154A- benzylpenicillin at pH 6
Analyse Crystal structure of the acyl-enzyme oxa-10 W154A- benzylpenicillin at pH 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WGI
- Type
- protein
- Length
- 481 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
- PNM
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase oxa-10 (EC 3.5.2.6) | protein | 234 | 41% helix, 22% strand | P14489 |
| B | Beta-lactamase oxa-10 (EC 3.5.2.6) | protein | 247 | 40% helix, 23% strand | P14489 |
Ligands and binding sites
- PNM · Open form - penicillin G · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.74 | 0.90 | 38 | empty |
| 2 | 178 | 0.74 | 0.91 | 34 | empty |
| 3 | 83 | 0.72 | 0.95 | 16 | empty |
| 4 | 150 | 0.49 | 0.78 | 21 | empty |
| 5 | 193 | 0.46 | 0.74 | 31 | PNM |
Interfaces
1 interface between chains.
- A–B · 1325 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 2WGI · Crystal structure of the acyl-enzyme OXA-10 W154A-benzylpenicillin at pH 6 · 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 2WGI · PDBe 2WGI · UniProt P14489
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