Research workbench
B-glucuronidase from ruminococcus gnavus in complex with uronic isofagomine at 1.3 ångströms resolution
Analyse B-glucuronidase from ruminococcus gnavus in complex with uronic isofagomine at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JZ2
- Type
- protein
- Length
- 1,185 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- UniProt
- Q6W7J7
- Ligands
- SJ5
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase | protein | 589 | 22% helix, 34% strand | Q6W7J7 |
| B | Beta-glucuronidase | protein | 596 | 22% helix, 34% strand | Q6W7J7 |
Ligands and binding sites
- SJ5 · (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid · ligand · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.86 | 0.87 | 103 | empty |
| 2 | 997 | 0.79 | 0.80 | 121 | SJ5, MPD |
| 3 | 182 | 0.71 | 0.88 | 19 | MRD |
| 4 | 349 | 0.67 | 0.81 | 39 | SJ5 |
| 5 | 53 | 0.48 | 0.85 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1633 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6JZ2 · b-glucuronidase from Ruminococcus gnavus in complex with uronic isofagomine at 1.3… · 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 6JZ2 · PDBe 6JZ2 · UniProt Q6W7J7
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