MolNFT v1 · #63807 · protein
Ampc K67R mutant complexed with BENZO(B)THIOPHENE-2-boronic acid (bzb)
3FKV · Beta-lactamase: “Ampc K67R mutant complexed with BENZO(B)THIOPHENE-2-boronic acid (bzb)”. X-ray diffraction, 3 ligands (BZB, K, PO4), 9 pockets (best druggability 0.77). MolNFT v1 #63807 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3FKV
- Type
- protein
- Length
- 714 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, K, PO4
- Pockets
- 9 · best druggability 0.77
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 | 356 | 38% helix, 23% strand | P00811 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 40% helix, 23% strand | P00811 |
Ligands and binding sites
- BZB · Benzo[b]thiophene-2-boronic acid · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.77 | 0.88 | 62 | empty |
| 2 | 360 | 0.65 | 0.80 | 47 | BZB |
| 3 | 459 | 0.64 | 0.77 | 50 | BZB |
| 4 | 186 | 0.55 | 0.80 | 35 | empty |
| 5 | 96 | 0.48 | 0.80 | 24 | K |
Interfaces
1 interface between chains.
- A–B · 836 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3FKV · AmpC K67R mutant complexed with benzo(b)thiophene-2-boronic acid (bzb) · 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 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
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 3FKV · PDBe 3FKV · UniProt P00811
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