MolNFT v1 · #119585 · protein
Beta-glucuronidase with an activity-based probe (N-acyl cyclophellitol aziridine) bound
5G0M: “Beta-glucuronidase with an activity-based probe (N-acyl cyclophellitol aziridine) bound”. X-ray diffraction, 2 ligands (J13, PO4), 4 pockets (best druggability 0.62). MolNFT v1 #119585 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5G0M
- Type
- protein
- Length
- 457 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- EC
- 3.2.1.31
- UniProt
- C1F2K5
- Ligands
- J13, PO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase (EC 3.2.1.31) | protein | 457 | 30% helix, 29% strand | C1F2K5 |
Ligands and binding sites
- J13 · (1S,2R,3R,4S,6S)-6-[(8-azidooctanoyl)amino]-2,3,4-trihydroxycyclohexane-1-carboxylate · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.62 | 0.80 | 38 | J13 |
| 2 | 206 | 0.51 | 0.77 | 46 | empty |
| 3 | 92 | 0.41 | 0.78 | 17 | empty |
| 4 | 64 | 0.30 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5G0M · beta-glucuronidase with an activity-based probe (N-acyl cyclophellitol aziridine) bound · 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 C1F2K5
- Elsewhere: RCSB PDB 5G0M · PDBe 5G0M · UniProt C1F2K5
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