MolNFT v1 · #141250 · protein
The crystal structure of ruminococcus gnavus beta-glucuronidase in complex with uronic isofagomine
5Z19: “The crystal structure of ruminococcus gnavus beta-glucuronidase in complex with uronic isofagomine”. X-ray diffraction, 1 ligand (SJ5), 20 pockets (best druggability 0.86). MolNFT v1 #141250 on GenesisL1: 3D structure, binding sites…
- PDB
- 5Z19
- Type
- protein
- Length
- 3,587 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- UniProt
- Q6W7J7
- Ligands
- SJ5
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase | protein | 593 | 21% helix, 33% strand | Q6W7J7 |
| B | Beta-glucuronidase | protein | 601 | 20% helix, 33% strand | Q6W7J7 |
| C, F | Beta-glucuronidase | protein | 600 | 21% helix, 33% strand | Q6W7J7 |
| D | Beta-glucuronidase | protein | 596 | 21% helix, 33% strand | Q6W7J7 |
| E | Beta-glucuronidase | protein | 597 | 21% helix, 33% strand | Q6W7J7 |
Ligands and binding sites
- SJ5 · (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.86 | 0.89 | 120 | SJ5 |
| 2 | 937 | 0.86 | 0.87 | 96 | empty |
| 3 | 815 | 0.84 | 0.86 | 88 | empty |
| 4 | 1099 | 0.78 | 0.80 | 95 | empty |
| 5 | 929 | 0.75 | 0.78 | 116 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1894 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1655 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1641 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 715 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 599 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5Z19 · The crystal structure of Ruminococcus gnavus beta-glucuronidase in complex with uronic… · 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 5Z19 · PDBe 5Z19 · UniProt Q6W7J7
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