Research workbench
X-ray crystal structure of the extended-spectrum ampc T70I mutant beta-lactamase with and without BENZO(B)THIOPHENE-2-boronic acid bound at 2.14 ångström resolution
Analyse X-ray crystal structure of the extended-spectrum ampc T70I mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IXG
- Type
- protein
- Length
- 675 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
- BZB
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 317 | 39% helix, 22% strand | P00811 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 38% helix, 23% strand | P00811 |
Ligands and binding sites
- BZB · Benzo[b]thiophene-2-boronic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.70 | 0.98 | 22 | empty |
| 2 | 327 | 0.61 | 0.78 | 28 | empty |
| 3 | 184 | 0.53 | 0.79 | 37 | empty |
| 4 | 205 | 0.49 | 0.76 | 31 | BZB |
| 5 | 221 | 0.48 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1111 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3IXG · X-ray crystal structure of the extended-spectrum AmpC T70I mutant beta-lactamase with and… · the same entry in another collection · 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 0.98
- 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 0.98
- 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 0.98
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 3IXG · PDBe 3IXG · UniProt P00811
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