MolNFT v1 · #131653 · protein
Oxa-48 in complex with compound 32
5QAY · Beta-lactamase: “Oxa-48 in complex with compound 32”. X-ray diffraction, 2 ligands (X6P, CL), 11 pockets (best druggability 0.78). MolNFT v1 #131653 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QAY
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- X6P, CL
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- X6P · 3-(1-methylpyrrol-2-yl)benzoic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.78 | 0.81 | 114 | X6P, CL |
| 2 | 707 | 0.78 | 0.82 | 94 | CL, EDO |
| 3 | 164 | 0.47 | 0.76 | 28 | empty |
| 4 | 195 | 0.45 | 0.74 | 23 | empty |
| 5 | 125 | 0.41 | 0.75 | 23 | X6P |
Interfaces
4 interfaces between chains.
- A–C · 966 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 964 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 255 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 172 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QAY · Oxa-48 in complex with compound 32 · 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 5QAY · PDBe 5QAY · UniProt Q6XEC0
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