MolNFT v1 · #131652 · protein
Oxa-48 in complex with compound 28
5QAX · Beta-lactamase: “Oxa-48 in complex with compound 28”. X-ray diffraction, 2 ligands (Q92, CL), 8 pockets (best druggability 0.81). MolNFT v1 #131652 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QAX
- 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
- Q92, CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 20% strand | Q6XEC0 |
Ligands and binding sites
- Q92 · 3-quinolin-6-ylbenzoic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.81 | 0.85 | 107 | CL, EDO |
| 2 | 813 | 0.78 | 0.81 | 117 | Q92, CL, EDO |
| 3 | 116 | 0.43 | 0.77 | 20 | Q92 |
| 4 | 51 | 0.40 | 0.82 | 15 | empty |
| 5 | 66 | 0.37 | 0.79 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 967 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 967 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 97 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QAX · Oxa-48 in complex with compound 28 · 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 5QAX · PDBe 5QAX · UniProt Q6XEC0
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