MolNFT v1 · #166610 · protein
Oxa-48 bound by inhibitor cdd-97
6UVK · Beta-lactamase: “Oxa-48 bound by inhibitor cdd-97”. X-ray diffraction, 2 ligands (QHY, CL), 9 pockets (best druggability 0.73). MolNFT v1 #166610 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6UVK
- 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
- QHY, CL
- Pockets
- 9 · best druggability 0.73
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
- QHY · 1-{4-[4-(2-ethoxyphenyl)piperazin-1-yl]-1,3,5-triazin-2-yl}piperidine-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.73 | 0.79 | 76 | EDO, GOL |
| 2 | 1099 | 0.71 | 0.75 | 112 | EDO, QHY |
| 3 | 506 | 0.67 | 0.78 | 48 | empty |
| 4 | 295 | 0.55 | 0.76 | 35 | QHY |
| 5 | 168 | 0.47 | 0.76 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–C · 399 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 380 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 275 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 258 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 142 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6UVK · OXA-48 bound by inhibitor CDD-97 · 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 6UVK · PDBe 6UVK · UniProt Q6XEC0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.