Research workbench
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 4-diphosphoinositol pentakisphosphate (4-IP7), mg, and fluoride ion
Analyse Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WOB
- Type
- protein
- Length
- 134 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphosphoinositol polyphosphate phosphohydrolase 1
- EC
- 3.6.1.52, 3.6.1.-
- UniProt
- O95989
- Ligands
- U71, MG, CL, F
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diphosphoinositol polyphosphate phosphohydrolase 1 (EC 3.6.1.52, 3.6.1.-) | protein | 134 | 24% helix, 40% strand | O95989 |
Ligands and binding sites
- U71 · (1S,2R,3S,4S,5S,6S)-2,3,4,5,6-pentakis(phosphonooxy) cyclohexyl trihydrogen diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- F · Fluoride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.48 | 0.75 | 38 | U71, MG, CL |
Compared structures
- 6WOB · Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O95989 · AlphaFold monomer V2.0 prediction for diphosphoinositol polyphosphate phosphohydrolase 1… · 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 O95989
- Elsewhere: RCSB PDB 6WOB · PDBe 6WOB · UniProt O95989
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