MolNFT v1 · #131656 · protein
Oxa-48 in complex with compound 36
5QB1 · Beta-lactamase: “Oxa-48 in complex with compound 36”. X-ray diffraction, 2 ligands (F1C, CL), 6 pockets (best druggability 0.79). MolNFT v1 #131656 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QB1
- 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
- F1C, CL
- Pockets
- 6 · best druggability 0.79
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
- F1C · 3,5-bis(3-acetamidophenyl)benzoic acid · ligand · 2 copies · chains B, D
- CL · Chloride ion · ion · 2 copies · chains A, D, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, D, B, C
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 | 558 | 0.79 | 0.85 | 84 | CL, EDO |
| 2 | 883 | 0.78 | 0.81 | 81 | EDO |
| 3 | 790 | 0.74 | 0.79 | 93 | empty |
| 4 | 117 | 0.37 | 0.74 | 22 | F1C |
| 5 | 50 | 0.37 | 0.80 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–D · 978 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 468 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 409 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 274 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QB1 · Oxa-48 in complex with compound 36 · 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 5QB1 · PDBe 5QB1 · UniProt Q6XEC0
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