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Crystal structure of the core catalytic domain of human inositol phosphate multikinase soaked with C4-analogue of PTDINS(4,5)P2 and ADP
Analyse Crystal structure of the core catalytic domain of human inositol phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W2I
- Type
- protein
- Length
- 239 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol polyphosphate MULTIKINASE,INOSITOL polyphosphate multikinase
- EC
- 2.7.1.151
- UniProt
- Q8NFU5
- Ligands
- ADP, I3P, MG
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol polyphosphate MULTIKINASE,INOSITOL polyphosphate multikinase (EC 2.7.1.151) | protein | 239 | 37% helix, 26% strand | Q8NFU5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- I3P · D-myo-inositol-1,4,5-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · 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 | 229 | 0.54 | 0.77 | 24 | ADP |
| 2 | 89 | 0.40 | 0.77 | 18 | MG, I3P |
Compared structures
- 5W2I · Crystal structure of the core catalytic domain of human inositol phosphate multikinase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NFU5 · AlphaFold monomer V2.0 prediction for inositol polyphosphate multikinase (Q8NFU5) · 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 Q8NFU5
- Elsewhere: RCSB PDB 5W2I · PDBe 5W2I · UniProt Q8NFU5
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