MolNFT v1 · #65251 · protein
Ampc beta-lactamase in complex with fragment-based inhibitor
3GRJ: “Ampc beta-lactamase in complex with fragment-based inhibitor”. X-ray diffraction, 2 ligands (G14, PO4), 10 pockets (best druggability 0.80). MolNFT v1 #65251 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GRJ
- Type
- protein
- Length
- 713 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
- G14, PO4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 355 | 40% helix, 24% strand | P00811 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 40% helix, 23% strand | P00811 |
Ligands and binding sites
- G14 · 2-phenyl-1H-imidazole-4-carboxylic acid · ligand · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.80 | 0.97 | 29 | empty |
| 2 | 317 | 0.67 | 0.82 | 59 | PO4, G14, PEG, DMS |
| 3 | 408 | 0.64 | 0.78 | 51 | PO4 |
| 4 | 218 | 0.61 | 0.81 | 38 | empty |
| 5 | 121 | 0.55 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3GRJ · AmpC beta-lactamase in complex with Fragment-based Inhibitor · 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 3GRJ · PDBe 3GRJ · UniProt P00811
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