MolNFT v1 · #131624 · protein
Oxa-48 in complex with compound 3B
5QA5 · Beta-lactamase: “Oxa-48 in complex with compound 3B”. X-ray diffraction, 2 ligands (L5D, CL), 9 pockets (best druggability 0.79). MolNFT v1 #131624 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QA5
- Type
- protein
- Length
- 969 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
- L5D, CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 20% strand | Q6XEC0 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 40% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- L5D · 3-(3-methylphenyl)benzoic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.79 | 0.80 | 94 | EDO |
| 2 | 924 | 0.76 | 0.79 | 98 | L5D, EDO |
| 3 | 209 | 0.52 | 0.77 | 29 | empty |
| 4 | 111 | 0.37 | 0.74 | 21 | L5D |
| 5 | 115 | 0.37 | 0.73 | 22 | L5D |
Interfaces
4 interfaces between chains.
- B–C · 451 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 425 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 271 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 265 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
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 5QA5 · PDBe 5QA5 · UniProt Q6XEC0
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