MolNFT v1 · #146098 · protein
The crystal structure of parabacteroides merdae beta-glucuronidase (gus) with glycerol in active-site
6D7J: “The crystal structure of parabacteroides merdae beta-glucuronidase (gus) with glycerol in active-site”. X-ray diffraction, 3 ligands (PRO, K, NA), 20 pockets (best druggability 0.74). MolNFT v1 #146098 on GenesisL1: 3D structure…
- PDB
- 6D7J
- Type
- protein
- Length
- 3,163 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- UniProt
- K5ZWV5
- Ligands
- PRO, K, NA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase | protein | 799 | 16% helix, 37% strand | K5ZWV5 |
| B | Beta-glucuronidase | protein | 788 | 16% helix, 38% strand | K5ZWV5 |
| C | Beta-glucuronidase | protein | 789 | 16% helix, 37% strand | K5ZWV5 |
| D | Beta-glucuronidase | protein | 787 | 16% helix, 37% strand | K5ZWV5 |
Ligands and binding sites
- PRO · Proline · ligand · 2 copies · chains A, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 53 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.74 | 0.77 | 98 | empty |
| 2 | 975 | 0.73 | 0.77 | 102 | GOL |
| 3 | 831 | 0.70 | 0.76 | 94 | GOL |
| 4 | 547 | 0.70 | 0.79 | 77 | GOL |
| 5 | 577 | 0.70 | 0.79 | 89 | GOL |
Interfaces
4 interfaces between chains.
- A–B · 1928 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1910 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 755 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 746 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6D7J · The Crystal Structure of Parabacteroides merdae Beta-Glucuronidase (GUS) with Glycerol in… · the same entry in another collection · chain B against B, 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 K5ZWV5
- Elsewhere: RCSB PDB 6D7J · PDBe 6D7J · UniProt K5ZWV5
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