MolNFT v1 · #97506 · protein
Crystal structure of ampc beta-lactamase N152G mutant in complex with cefotaxime
4KG5: “Crystal structure of ampc beta-lactamase N152G mutant in complex with cefotaxime”. X-ray diffraction, 2 ligands (CEF, PO4), 18 pockets (best druggability 0.78). MolNFT v1 #97506 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4KG5
- Type
- protein
- Length
- 1,432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P00811
- Ligands
- CEF, PO4
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 40% helix, 23% strand | P00811 |
Ligands and binding sites
- CEF · CEFOTAXIME, C3' cleaved, open, bound form · ligand · 4 copies · chains B, A, C, D
- PO4 · Phosphate ion · ion · 5 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.78 | 0.82 | 88 | CEF |
| 2 | 430 | 0.78 | 0.87 | 51 | empty |
| 3 | 474 | 0.78 | 0.86 | 65 | empty |
| 4 | 1008 | 0.78 | 0.80 | 108 | CEF |
| 5 | 401 | 0.71 | 0.82 | 59 | CEF |
Interfaces
4 interfaces between chains.
- A–D · 703 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 646 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 624 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 447 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4KG5 · Crystal Structure of AmpC beta-lactamase N152G Mutant in Complex with Cefotaxime · 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 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
- 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
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 4KG5 · PDBe 4KG5 · UniProt P00811
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