Research workbench
Apo structure of bacteroides uniformis beta-glucuronidase 3
Analyse Apo structure of bacteroides uniformis beta-glucuronidase 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D1P
- Type
- protein
- Length
- 1,560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolases family 2, sugar binding domain protein
- UniProt
- A0A078SSU5
- Ligands
- NA, K, SCN
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolases family 2, sugar binding domain protein | protein | 781 | 16% helix, 36% strand | A0A078SSU5 |
| B | Glycosyl hydrolases family 2, sugar binding domain protein | protein | 779 | 17% helix, 36% strand | A0A078SSU5 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- SCN · Thiocyanate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.71 | 0.81 | 42 | empty |
| 2 | 939 | 0.71 | 0.76 | 116 | empty |
| 3 | 477 | 0.69 | 0.80 | 47 | empty |
| 4 | 194 | 0.60 | 0.82 | 32 | GOL, SCN |
| 5 | 236 | 0.59 | 0.80 | 37 | GOL |
Interfaces
1 interface between chains.
- A–B · 1932 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6D1P · Apo structure of Bacteroides uniformis beta-glucuronidase 3 · 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 A0A078SSU5
- Elsewhere: RCSB PDB 6D1P · PDBe 6D1P · UniProt A0A078SSU5
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