MolNFT v1 · #115975 · protein
Structure of E. COLI beta-glucuronidase bound with a novel, potent inhibitor 1-((6,8-dimethyl-2-oxo-1,2-dihydroquinolin-3-YL)METHYL)-1- (2-hydroxyethyl)-3-(4-HYDROXYPHENYL)THIOUREA
5CZK: “Structure of E. COLI beta-glucuronidase bound with a novel, potent inhibitor…”. X-ray diffraction, 1 ligand (57Z), 15 pockets (best druggability 0.87). MolNFT v1 #115975 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CZK
- Type
- protein
- Length
- 1,201 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- EC
- 3.2.1.31
- UniProt
- P05804
- Ligands
- 57Z
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase (EC 3.2.1.31) | protein | 600 | 21% helix, 30% strand | P05804 |
| B | Beta-glucuronidase (EC 3.2.1.31) | protein | 601 | 21% helix, 30% strand | P05804 |
Ligands and binding sites
- 57Z · 1-[(6,8-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl]-1-(2-hydroxyethyl)-3-(4-hydroxyphenyl)thiourea · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.87 | 0.89 | 109 | empty |
| 2 | 106 | 0.75 | 0.95 | 21 | empty |
| 3 | 57 | 0.72 | 0.98 | 19 | empty |
| 4 | 56 | 0.71 | 0.98 | 21 | empty |
| 5 | 531 | 0.70 | 0.80 | 57 | 57Z |
Interfaces
1 interface between chains.
- A–B · 1624 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 5CZK · Structure of E. coli beta-glucuronidase bound with a novel, potent inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P05804 · AlphaFold monomer V2.0 prediction for beta-glucuronidase (P05804) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P05804
- Elsewhere: RCSB PDB 5CZK · PDBe 5CZK · UniProt P05804
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