MolNFT v1 · #160057 · protein
Oxa-48 carbapanemase, doripenem complex
6P9C · Beta-lactamase: “Oxa-48 carbapanemase, doripenem complex”. X-ray diffraction, 5 ligands (4J6, O6P, CA), 3 pockets (best druggability 0.77). MolNFT v1 #160057 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6P9C
- 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
- 4J6, O6P, CA, CD, CL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- 4J6 · (4R,5S)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-3-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · 2 copies · chains A, B
- O6P · Doripenem · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.77 | 0.80 | 121 | 4J6, CL |
| 2 | 61 | 0.44 | 0.83 | 20 | empty |
| 3 | 50 | 0.34 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1011 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6P9C · OXA-48 carbapanemase, doripenem complex · 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 6P9C · PDBe 6P9C · UniProt Q6XEC0
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