Research workbench
Ampc beta-lactamase from E. COLI complexed with inhibitor, BENZO(B) thiophene-2-boronic acid (bzb)
Analyse Ampc beta-lactamase from E. COLI complexed with inhibitor, BENZO(B)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C3B
- Type
- protein
- Length
- 716 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cephalosporinase
- EC
- 3.5.2.6
- UniProt
- P00811
- Ligands
- BZB
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cephalosporinase (EC 3.5.2.6) | protein | 358 | 41% helix, 23% strand | P00811 |
Ligands and binding sites
- BZB · Benzo[b]thiophene-2-boronic 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 | 584 | 0.81 | 0.86 | 75 | empty |
| 2 | 409 | 0.68 | 0.81 | 56 | BZB |
| 3 | 337 | 0.67 | 0.82 | 55 | BZB |
| 4 | 80 | 0.46 | 0.81 | 23 | empty |
| 5 | 76 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 810 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1C3B · Ampc beta-lactamase from E. COLI complexed with inhibitor, BENZO(B)THIOPHENE-2-boronic… · the same entry in another collection · chain A against A, 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 A against B, TM-score 1.00
- P00811 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00811) · a predicted model of the same protein · 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 P00811
- Elsewhere: RCSB PDB 1C3B · PDBe 1C3B · UniProt P00811
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