Research workbench
Crystal structure of class a beta-lactamase from bacillus licheniformis BS3 with clavulanic acid
Analyse Crystal structure of class a beta-lactamase from bacillus licheniformis BS3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y91
- Type
- protein
- Length
- 514 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
- 98J
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 257 | 43% helix, 19% strand | P94458 |
Ligands and binding sites
- 98J · 5-hydroxy-3-oxopentanoic acid · ligand · 3 copies · chains A, B
- CIT · Citric acid · additive · chains A
- PGE · Triethylene glycol · additive · chains A
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 | 308 | 0.66 | 0.82 | 54 | empty |
| 2 | 68 | 0.41 | 0.80 | 16 | empty |
| 3 | 84 | 0.40 | 0.78 | 16 | PGE |
| 4 | 93 | 0.39 | 0.76 | 22 | empty |
| 5 | 64 | 0.25 | 0.71 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 696 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 2Y91 · Crystal structure of class A beta-lactamase from Bacillus licheniformis BS3 with… · 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 2Y91 · PDBe 2Y91 · UniProt P94458
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