Research workbench
X-ray crystal structure of ampc beta-lactamase from E. COLI in complex with the inhibitor 3-nitrophenylboronic acid
Analyse X-ray crystal structure of ampc beta-lactamase from E. COLI in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KDS
- Type
- protein
- Length
- 716 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P00811
- Ligands
- NPB
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 38% helix, 23% strand | P00811 |
Ligands and binding sites
- NPB · 3-nitrophenylboronic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.78 | 0.86 | 58 | empty |
| 2 | 321 | 0.67 | 0.82 | 48 | NPB |
| 3 | 320 | 0.65 | 0.81 | 51 | NPB |
| 4 | 225 | 0.52 | 0.77 | 37 | empty |
| 5 | 100 | 0.49 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 662 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1KDS · X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the 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
- 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 1KDS · PDBe 1KDS · UniProt P00811
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