MolNFT v1 · #179827 · protein
Crystal structure of oxa-48 K73A in complex with imipenem
7KH9 · Beta-lactamase: “Crystal structure of oxa-48 K73A in complex with imipenem”. X-ray diffraction, 2 ligands (IM2, CL), 4 pockets (best druggability 0.77). MolNFT v1 #179827 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KH9
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- IM2, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid · ligand · 2 copies · chains B, A
- CL · Chloride ion · ion · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.77 | 0.82 | 103 | CL, IM2 |
| 2 | 62 | 0.39 | 0.80 | 18 | empty |
| 3 | 59 | 0.39 | 0.80 | 17 | empty |
| 4 | 112 | 0.38 | 0.75 | 19 | IM2 |
Interfaces
1 interface between chains.
- B–A · 995 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7KH9 · Crystal structure of OXA-48 K73A in complex with imipenem · the same entry in another collection · chain A 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 Q6XEC0
- Elsewhere: RCSB PDB 7KH9 · PDBe 7KH9 · UniProt Q6XEC0
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