MolNFT v1 · #152029 · protein
Crystal structure of an oxa-48 beta-lactamase synthetic mutant
6I5D: “Crystal structure of an oxa-48 beta-lactamase synthetic mutant”. X-ray diffraction, 3 ligands (NO3, CL, PO4), 4 pockets (best druggability 0.78). MolNFT v1 #152029 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6I5D
- Type
- protein
- Length
- 487 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
- NO3, CL, PO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 244 | 39% helix, 18% strand | Q6XEC0 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 40% helix, 19% strand | Q6XEC0 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 13 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
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 | 540 | 0.78 | 0.85 | 86 | GOL, CL, EDO, PEG |
| 2 | 77 | 0.44 | 0.81 | 18 | GOL |
| 3 | 65 | 0.36 | 0.78 | 17 | empty |
| 4 | 71 | 0.36 | 0.77 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 994 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6I5D · Crystal structure of an OXA-48 beta-lactamase synthetic mutant · 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 6I5D · PDBe 6I5D · UniProt Q6XEC0
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