MolNFT v1 · #104234 · protein
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and synthetic 1,5-(PP)2-IP4 (1,5-IP8)
4Q4C · Inositol hexakisphosphate and diphosphoinositol…: “Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in…”. X-ray diffraction, 3 ligands (ADP, I8P, MG), 2 pockets (best…
- PDB
- 4Q4C
- Type
- protein
- Length
- 325 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol hexakisphosphate and diphosphoinositol- pentakisphosphate kinase 2
- EC
- 2.7.4.21, 2.7.4.24
- UniProt
- O43314
- Ligands
- ADP, I8P, MG
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol hexakisphosphate and diphosphoinositol- pentakisphosphate kinase 2 (EC 2.7.4.21, 2.7.4.24) | protein | 325 | 27% helix, 31% strand | O43314 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- I8P · (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy) cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)] · ligand · chains A
- MG · Magnesium ion · metal · 5 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 | 840 | 0.81 | 0.83 | 77 | ADP, I8P, MG |
| 2 | 106 | 0.38 | 0.75 | 24 | empty |
Compared structures
- 4Q4C · Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- O43314 · AlphaFold monomer V2.0 prediction for inositol hexakisphosphate and… · 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 O43314
- Elsewhere: RCSB PDB 4Q4C · PDBe 4Q4C · UniProt O43314
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