MolNFT v1 · #53098 · protein
Crystal structure of the oxa-10 K70C mutant at pH 7.0
2WKI · Beta-lactamase oxa-10: “Crystal structure of the oxa-10 K70C mutant at pH 7.0”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.71). MolNFT v1 #53098 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WKI
- Type
- protein
- Length
- 491 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
- SO4
- Pockets
- 5 · best druggability 0.71
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 | 244 | 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
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.71 | 0.89 | 33 | GOL |
| 2 | 171 | 0.70 | 0.89 | 31 | GOL |
| 3 | 170 | 0.45 | 0.75 | 29 | SO4 |
| 4 | 149 | 0.43 | 0.75 | 24 | SO4 |
| 5 | 54 | 0.30 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1251 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 2WKI · PDBe 2WKI · UniProt P14489
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