Research workbench
Chemical dissection of the link between streptozotocin, O-glcnac and pancreatic cell death
Analyse Chemical dissection of the link between streptozotocin, O-glcnac and pancreatic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VUR
- Type
- protein
- Length
- 1,168 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase nagj
- EC
- 3.2.1.35
- UniProt
- Q0TR53
- Ligands
- YX1, SO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-glcnacase nagj (EC 3.2.1.35) | protein | 584 | 47% helix, 15% strand | Q0TR53 |
Ligands and binding sites
- YX1 · 2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucopyranose · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.77 | 0.79 | 83 | empty |
| 2 | 385 | 0.73 | 0.84 | 49 | YX1 |
| 3 | 465 | 0.70 | 0.81 | 57 | YX1 |
| 4 | 155 | 0.50 | 0.78 | 29 | empty |
| 5 | 147 | 0.50 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 922 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2VUR · Chemical dissection of the link between Streptozotocin, O-GlcNAc and pancreatic cell death · the same entry in another collection · chain A against A, TM-score 1.00
- Q0TR53 · AlphaFold monomer V2.0 prediction for O-glcnacase nagj (Q0TR53) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q0TR53
- Elsewhere: RCSB PDB 2VUR · PDBe 2VUR · UniProt Q0TR53
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