Research workbench
Bacteroides dorei beta-glucuronidase
Analyse Bacteroides dorei beta-glucuronidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ED1
- Type
- protein
- Length
- 3,440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 2, sugar binding domain protein
- UniProt
- C3R9X4
- Ligands
- NA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycosyl hydrolase family 2, sugar binding domain protein | protein | 860 | 15% helix, 38% strand | C3R9X4 |
Ligands and binding sites
- NA · Sodium 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.84 | 0.85 | 95 | empty |
| 2 | 1133 | 0.84 | 0.85 | 106 | empty |
| 3 | 132 | 0.79 | 0.96 | 38 | empty |
| 4 | 695 | 0.78 | 0.83 | 65 | empty |
| 5 | 1147 | 0.77 | 0.79 | 80 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3642 Ų buried · 79 hydrogen bonds · protein-protein
- A–B · 660 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 434 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 410 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 147 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ED1 · Bacteroides dorei 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 C3R9X4
- Elsewhere: RCSB PDB 6ED1 · PDBe 6ED1 · UniProt C3R9X4
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