Research workbench
X-ray crystal structure of AmpC beta-lactamase with inhibitor
Analyse X-ray crystal structure of AmpC beta-lactamase with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DPX
- Type
- protein
- Length
- 716 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Escherichia coli (strain K12)
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P00811
- Ligands
- H7G
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 40% helix, 23% strand | P00811 |
Ligands and binding sites
- H7G · (3-{[(3-chloro-2-hydroxyphenyl)sulfonyl]amino}phenyl) acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.78 | 0.87 | 59 | empty |
| 2 | 360 | 0.67 | 0.81 | 54 | H7G |
| 3 | 304 | 0.63 | 0.80 | 51 | H7G |
| 4 | 67 | 0.47 | 0.83 | 20 | empty |
| 5 | 79 | 0.31 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 694 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6DPX · X-ray crystal structure of ampc beta-lactamase with inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
- 1L2S · X-ray crystal structure of ampc beta-lactamase from E. COLI in complex with a… · a predicted model of the same protein · chain B against B, TM-score 1.00
- 1L2S · X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with a… · a predicted model of the same protein · chain B against B, TM-score 1.00
- P00811 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00811) · a predicted model of the same protein · chain B 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 P00811
- Elsewhere: RCSB PDB 6DPX · PDBe 6DPX · UniProt P00811
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