MolNFT v1 · #53097 · protein
Crystal structure of the acyl-enzyme oxa-10 K70C-ampicillin at pH 7
2WKH · Beta-lactamase oxa-10: “Crystal structure of the acyl-enzyme oxa-10 K70C-ampicillin at pH 7”. X-ray diffraction, 2 ligands (ZZ7, SO4), 4 pockets (best druggability 0.72). MolNFT v1 #53097 on GenesisL1: 3D structure, binding sites…
- PDB
- 2WKH
- Type
- protein
- Length
- 490 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
- ZZ7, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase oxa-10 (EC 3.5.2.6) | protein | 244 | 41% helix, 24% strand | P14489 |
| B | Beta-lactamase oxa-10 (EC 3.5.2.6) | protein | 246 | 39% helix, 24% strand | P14489 |
Ligands and binding sites
- ZZ7 · (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.72 | 0.90 | 32 | empty |
| 2 | 102 | 0.64 | 0.89 | 30 | empty |
| 3 | 155 | 0.43 | 0.75 | 25 | ZZ7, SO4 |
| 4 | 144 | 0.43 | 0.76 | 25 | ZZ7, SO4 |
Interfaces
1 interface between chains.
- A–B · 1317 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 2WKH · Crystal structure of the acyl-enzyme OXA-10 K70C-Ampicillin at pH 7 · 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 2WKH · PDBe 2WKH · UniProt P14489
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