MolNFT v1 · #131657 · protein
Oxa-48 in complex with compound 38
5QB2 · Beta-lactamase: “Oxa-48 in complex with compound 38”. X-ray diffraction, 2 ligands (U3M, CL), 9 pockets (best druggability 0.78). MolNFT v1 #131657 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QB2
- 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
- U3M, CL
- Pockets
- 9 · 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
- U3M · 3-quinolin-6-yl-5-quinolin-7-yl-benzoic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.78 | 0.80 | 94 | empty |
| 2 | 915 | 0.76 | 0.79 | 97 | U3M, EDO |
| 3 | 190 | 0.48 | 0.75 | 26 | empty |
| 4 | 105 | 0.36 | 0.74 | 20 | empty |
| 5 | 104 | 0.35 | 0.73 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 480 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 428 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 264 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 242 Ų buried · 0 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 5QB2 · PDBe 5QB2 · UniProt Q6XEC0
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