Research workbench
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and mg, presoaked with 5-IP7, mg and fluoride, soaking 2MIN in the absence of fluoride.
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
- 6WOD
- 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
- IHP, MG, CL
- Pockets
- 1 · best druggability 0.44
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
- IHP · Inositol hexakisphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · 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 | 171 | 0.44 | 0.74 | 29 | MG, CL, IHP |
Compared structures
- 6WOD · Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol… · 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 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 O95989
- Elsewhere: RCSB PDB 6WOD · PDBe 6WOD · UniProt O95989
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