Research workbench
The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation
Analyse The structure of vanin-1: defining the link between metabolic disease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CYF
- Type
- protein
- Length
- 924 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantetheinase
- EC
- 3.5.1.92
- UniProt
- O95497
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pantetheinase (EC 3.5.1.92) | protein | 462 | 18% helix, 35% strand | O95497 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.71 | 0.81 | 68 | empty |
| 2 | 174 | 0.66 | 0.85 | 25 | empty |
| 3 | 205 | 0.65 | 0.84 | 38 | empty |
| 4 | 228 | 0.53 | 0.77 | 40 | empty |
| 5 | 111 | 0.43 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 738 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 7 glycan, 2 modified (disulfide, N-glycosylation, oxidation).
Compared structures
- 4CYF · The structure of vanin-1: defining the link between metabolic disease, oxidative stress… · the same entry in another collection · chain A against A, TM-score 1.00
- O95497 · AlphaFold monomer V2.0 prediction for pantetheinase (O95497) · a predicted model of the same protein · 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 O95497
- Elsewhere: RCSB PDB 4CYF · PDBe 4CYF · UniProt O95497
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.