Research workbench
Beta-glucuronidase with an activity-based probe (N-alkyl cyclophellitol aziridine) bound
Analyse Beta-glucuronidase with an activity-based probe (N-alkyl cyclophellitol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G0Q
- Type
- protein
- Length
- 455 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
- IF6
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase (EC 3.2.1.31) | protein | 455 | 30% helix, 27% strand | C1F2K5 |
Ligands and binding sites
- IF6 · (1R,2S,3R,4S,5S,6R)-7-(8-azidooctyl)-3,4,5-trihydroxy- · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.64 | 0.80 | 40 | IF6 |
| 2 | 95 | 0.46 | 0.80 | 26 | empty |
| 3 | 100 | 0.43 | 0.78 | 19 | empty |
| 4 | 60 | 0.30 | 0.75 | 17 | empty |
| 5 | 65 | 0.28 | 0.73 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5G0Q · beta-glucuronidase with an activity-based probe (N-alkyl 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 5G0Q · PDBe 5G0Q · UniProt C1F2K5
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