MolNFT v1 · #131639 · protein
Oxa-48 in complex with compound 14
5QAK · Beta-lactamase: “Oxa-48 in complex with compound 14”. X-ray diffraction, 2 ligands (AV4, CL), 11 pockets (best druggability 0.75). MolNFT v1 #131639 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QAK
- 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
- AV4, CL
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 20% strand | Q6XEC0 |
Ligands and binding sites
- AV4 · 3-[3-(dimethylamino)phenyl]benzoic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.75 | 0.81 | 77 | AV4, EDO |
| 2 | 474 | 0.73 | 0.82 | 53 | empty |
| 3 | 374 | 0.65 | 0.79 | 42 | empty |
| 4 | 172 | 0.50 | 0.77 | 26 | empty |
| 5 | 51 | 0.41 | 0.82 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 491 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 362 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 264 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 258 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QAK · Oxa-48 in complex with compound 14 · 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 5QAK · PDBe 5QAK · UniProt Q6XEC0
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