MolNFT v1 · #165820 · protein
Uncultured clostridium sp. beta-glucuronidase
6U7J: “Uncultured clostridium sp. beta-glucuronidase”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.88). MolNFT v1 #165820 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6U7J
- Type
- protein
- Length
- 2,277 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- EC
- 3.2.1.31
- UniProt
- A0A1C5YG41
- Ligands
- CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Beta-glucuronidase (EC 3.2.1.31) | protein | 569 | 21% helix, 34% strand | A0A1C5YG41 |
| B | Beta-glucuronidase (EC 3.2.1.31) | protein | 570 | 21% helix, 34% strand | A0A1C5YG41 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.88 | 0.90 | 124 | empty |
| 2 | 1178 | 0.87 | 0.88 | 106 | empty |
| 3 | 1123 | 0.87 | 0.88 | 115 | empty |
| 4 | 63 | 0.73 | 0.99 | 17 | empty |
| 5 | 683 | 0.71 | 0.78 | 73 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2154 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 2107 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1382 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1308 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 637 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6U7J · Uncultured Clostridium sp. 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 A0A1C5YG41
- Elsewhere: RCSB PDB 6U7J · PDBe 6U7J · UniProt A0A1C5YG41
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