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Refined crystal structure of beta-lactamase from citrobacter freundii indicates a mechanism for beta-lactam hydrolysis
Analyse Refined crystal structure of beta-lactamase from citrobacter freundii indicates… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FR6
- Type
- protein
- Length
- 722 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q46041
- Ligands
- AZR
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 361 | 37% helix, 23% strand | Q46041 |
Ligands and binding sites
- AZR · 2-({[(1Z)-1-(2-amino-1,3-thiazol-4-yl)-2-oxo-2-{[(2S, 3S)-1-oxo-3-(sulfoamino)butan-2-yl]amino}ethylidene]amino}oxy)-2-methylpropanoic acid · ligand · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.87 | 0.88 | 142 | AZR |
| 2 | 168 | 0.44 | 0.74 | 31 | empty |
| 3 | 130 | 0.42 | 0.75 | 21 | empty |
| 4 | 50 | 0.38 | 0.81 | 14 | empty |
| 5 | 59 | 0.35 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1312 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1FR6 · Refined crystal structure of beta-lactamase from citrobacter freundii indicates a… · 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 Q46041
- Elsewhere: RCSB PDB 1FR6 · PDBe 1FR6 · UniProt Q46041
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