MolNFT v1 · #131628 · protein
Oxa-48 in complex with compound 5
5QA9 · Beta-lactamase: “Oxa-48 in complex with compound 5”. X-ray diffraction, 2 ligands (QKU, CL), 6 pockets (best druggability 0.78). MolNFT v1 #131628 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QA9
- 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
- QKU, CL
- Pockets
- 6 · 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
- QKU · 3-[3-(hydroxymethyl)phenyl]benzoic acid · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.78 | 0.80 | 90 | EDO |
| 2 | 898 | 0.75 | 0.79 | 100 | QKU, EDO |
| 3 | 169 | 0.50 | 0.78 | 27 | empty |
| 4 | 163 | 0.44 | 0.74 | 28 | QKU |
| 5 | 102 | 0.36 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 439 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 408 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 302 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 275 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QA9 · Oxa-48 in complex with compound 5 · 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 5QA9 · PDBe 5QA9 · UniProt Q6XEC0
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