MolNFT v1 · #67872 · protein
X-ray crystal structure of the extended-spectrum ampc E219K mutant beta-lactamase complexed with BENZO(B)THIOPHENE-2-boronic acid (bzb) at 1.63 ångström resolution
3IXB: “X-ray crystal structure of the extended-spectrum ampc E219K mutant beta-lactamase complexed with…”. X-ray diffraction, 2 ligands (BZB, PO4), 7 pockets (best druggability 0.78). MolNFT v1 #67872 on GenesisL1: 3D structure, binding…
- PDB
- 3IXB
- Type
- protein
- Length
- 710 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, PO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 41% helix, 23% strand | P00811 |
| A | Beta-lactamase (EC 3.5.2.6) | protein | 352 | 39% helix, 24% strand | P00811 |
Ligands and binding sites
- BZB · Benzo[b]thiophene-2-boronic acid · ligand · 2 copies · chains B, A
- PO4 · Phosphate ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.78 | 0.91 | 51 | empty |
| 2 | 373 | 0.67 | 0.80 | 49 | BZB |
| 3 | 527 | 0.65 | 0.77 | 55 | BZB |
| 4 | 64 | 0.47 | 0.84 | 21 | empty |
| 5 | 90 | 0.46 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- B–A · 932 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3IXB · X-ray crystal structure of the extended-spectrum AmpC E219K mutant beta-lactamase… · 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 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 3IXB · PDBe 3IXB · UniProt P00811
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