MolNFT v1 · #154068 · protein
B-glucuronidase from ruminococcus gnavus in complex with N1- substituted uronic isofagomine
6JZ7 · Beta-glucuronidase: “B-glucuronidase from ruminococcus gnavus in complex with N1- substituted uronic isofagomine”. X-ray diffraction, 1 ligand (CKU), 14 pockets (best druggability 0.86). MolNFT v1 #154068 on GenesisL1: 3D structure…
- PDB
- 6JZ7
- Type
- protein
- Length
- 1,140 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- UniProt
- Q6W7J7
- Ligands
- CKU
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase | protein | 571 | 22% helix, 36% strand | Q6W7J7 |
| B | Beta-glucuronidase | protein | 569 | 21% helix, 36% strand | Q6W7J7 |
Ligands and binding sites
- CKU · (3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)-1-propyl-piperidine-3-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.86 | 0.87 | 88 | empty |
| 2 | 729 | 0.72 | 0.78 | 93 | empty |
| 3 | 214 | 0.57 | 0.79 | 26 | CKU |
| 4 | 183 | 0.55 | 0.80 | 29 | CKU |
| 5 | 58 | 0.54 | 0.88 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1614 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6JZ7 · b-glucuronidase from Ruminococcus gnavus in complex with N1-substituted uronic isofagomine · 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 Q6W7J7
- Elsewhere: RCSB PDB 6JZ7 · PDBe 6JZ7 · UniProt Q6W7J7
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