MolNFT v1 · #117008 · protein
Fragments bound to the oxa-48 beta-lactamase: compound 1
5DVA: “Fragments bound to the oxa-48 beta-lactamase: compound 1”. X-ray diffraction, 2 ligands (5FL, CL), 9 pockets (best druggability 0.74). MolNFT v1 #117008 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DVA
- 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
- 5FL, CL
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 20% strand | Q6XEC0 |
Ligands and binding sites
- 5FL · 3-(pyridin-4-yl)benzoic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.74 | 0.77 | 98 | 5FL |
| 2 | 657 | 0.72 | 0.79 | 63 | empty |
| 3 | 342 | 0.65 | 0.80 | 40 | empty |
| 4 | 162 | 0.47 | 0.77 | 23 | empty |
| 5 | 106 | 0.37 | 0.74 | 18 | 5FL |
Interfaces
4 interfaces between chains.
- A–B · 417 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 379 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 262 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 224 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5DVA · Fragments bound to the OXA-48 beta-lactamase: Compound 1 · 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 5DVA · PDBe 5DVA · UniProt Q6XEC0
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