Research workbench
Sirtuin 4 orthologue from xenopus tropicalis in complex with ADP- ribose
Analyse Sirtuin 4 orthologue from xenopus tropicalis in complex with ADP- ribose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OJ7
- Type
- protein
- Length
- 286 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase
- EC
- 3.5.1.-
- UniProt
- Q28CB4
- Ligands
- AR6, ZN
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 286 | 37% helix, 15% strand | Q28CB4 |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.78 | 0.86 | 64 | AR6, EDO, GOL |
| 2 | 77 | 0.32 | 0.74 | 20 | EDO |
Compared structures
- 5OJ7 · Sirtuin 4 orthologue from Xenopus Tropicalis in complex with ADP-ribose · 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 Q28CB4
- Elsewhere: RCSB PDB 5OJ7 · PDBe 5OJ7 · UniProt Q28CB4
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