MolNFT v1 · #53080 · protein
Crystal structure of the class a beta-lactamase BS3 inhibited by 6-beta-iodopenicillanate.
2WK0: “Crystal structure of the class a beta-lactamase BS3 inhibited by 6-beta-iodopenicillanate.”. X-ray diffraction, 3 ligands (BIY, CL, SO4), 5 pockets (best druggability 0.54). MolNFT v1 #53080 on GenesisL1: 3D structure, binding sites…
- PDB
- 2WK0
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P94458
- Ligands
- BIY, CL, SO4
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 255 | 42% helix, 19% strand | P94458 |
Ligands and binding sites
- BIY · (3S)-2,2-dimethyl-3,4-dihydro-2H-1,4-thiazine-3,6-dicarboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EOH · Ethanol · additive · 4 copies · chains A, B
- CIT · Citric acid · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.54 | 0.77 | 31 | empty |
| 2 | 86 | 0.44 | 0.80 | 17 | EOH |
| 3 | 64 | 0.42 | 0.82 | 17 | EOH |
| 4 | 58 | 0.30 | 0.76 | 15 | BIY, CL |
| 5 | 73 | 0.29 | 0.74 | 15 | BIY, CL |
Interfaces
1 interface between chains.
- A–B · 645 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2WK0 · Crystal structure of the class A beta-lactamase BS3 inhibited by 6… · 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 P94458
- Elsewhere: RCSB PDB 2WK0 · PDBe 2WK0 · UniProt P94458
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