Research workbench
The crystal structure of ruminococcus gnavus beta-glucuronidase
Analyse The crystal structure of ruminococcus gnavus beta-glucuronidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z18
- Type
- protein
- Length
- 3,519 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- UniProt
- Q6W7J7
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucuronidase | protein | 586 | 20% helix, 34% strand | Q6W7J7 |
| C | Beta-glucuronidase | protein | 588 | 20% helix, 34% strand | Q6W7J7 |
| D | Beta-glucuronidase | protein | 591 | 21% helix, 34% strand | Q6W7J7 |
| E | Beta-glucuronidase | protein | 586 | 21% helix, 34% strand | Q6W7J7 |
| F | Beta-glucuronidase | protein | 582 | 20% helix, 35% strand | Q6W7J7 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.86 | 0.87 | 97 | empty |
| 2 | 819 | 0.84 | 0.86 | 81 | empty |
| 3 | 1179 | 0.82 | 0.83 | 154 | empty |
| 4 | 1084 | 0.75 | 0.78 | 110 | empty |
| 5 | 173 | 0.73 | 0.90 | 23 | empty |
Interfaces
7 interfaces between chains.
- C–F · 1853 Ų buried · 27 hydrogen bonds · protein-protein
- C–E · 1596 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1582 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 622 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 614 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5Z18 · The crystal structure of Ruminococcus gnavus beta-glucuronidase · 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 5Z18 · PDBe 5Z18 · UniProt Q6W7J7
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