MolNFT v1 · #131647 · protein
Oxa-48 in complex with compound 23B
5QAS · Beta-lactamase: “Oxa-48 in complex with compound 23B”. X-ray diffraction, 1 ligand (CVF), 8 pockets (best druggability 0.79). MolNFT v1 #131647 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QAS
- 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
- CVF
- Pockets
- 8 · 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
- CVF · 3-[4-(2-acetamidoethyl)phenyl]benzoic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.79 | 0.82 | 92 | empty |
| 2 | 608 | 0.74 | 0.81 | 89 | CVF |
| 3 | 201 | 0.51 | 0.77 | 27 | empty |
| 4 | 107 | 0.36 | 0.74 | 24 | CVF |
| 5 | 101 | 0.35 | 0.74 | 19 | CVF |
Interfaces
5 interfaces between chains.
- A–B · 473 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 427 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 298 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 269 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QAS · OXA-48 IN COMPLEX WITH COMPOUND 23b · 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 5QAS · PDBe 5QAS · UniProt Q6XEC0
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