MolNFT v1 · #131651 · protein
Oxa-48 in complex with compound 27
5QAW · Beta-lactamase: “Oxa-48 in complex with compound 27”. X-ray diffraction, 2 ligands (TVC, CL), 9 pockets (best druggability 0.78). MolNFT v1 #131651 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QAW
- Type
- protein
- Length
- 967 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
- TVC, CL
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 20% strand | Q6XEC0 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 41% helix, 20% strand | Q6XEC0 |
Ligands and binding sites
- TVC · 3-naphthalen-2-ylbenzoic acid · ligand · 3 copies · chains A, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B
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 | 777 | 0.78 | 0.82 | 86 | empty |
| 2 | 698 | 0.76 | 0.81 | 92 | TVC |
| 3 | 156 | 0.46 | 0.76 | 24 | empty |
| 4 | 98 | 0.36 | 0.74 | 19 | TVC |
| 5 | 93 | 0.35 | 0.74 | 20 | TVC |
Interfaces
4 interfaces between chains.
- A–B · 433 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 346 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 278 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 258 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5QAW · Oxa-48 in complex with compound 27 · 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 5QAW · PDBe 5QAW · UniProt Q6XEC0
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