MolNFT v1 · #104235 · protein
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-pnp and synthetic 3,5-(PP)2-IP4 (3,5-IP8)
4Q4D · Inositol hexakisphosphate and diphosphoinositol…: “Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in…”. X-ray diffraction, 3 ligands (ANP, 2YN, MG), 1 pocket (best…
- PDB
- 4Q4D
- Type
- protein
- Length
- 317 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
- ANP, 2YN, MG
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 32% 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 | 317 | 28% helix, 32% strand | O43314 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- 2YN · (1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)] · ligand · chains A
- MG · Magnesium ion · metal · 3 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.78 | 0.81 | 68 | ANP, 2YN, MG |
Compared structures
- 4Q4D · 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 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 O43314
- Elsewhere: RCSB PDB 4Q4D · PDBe 4Q4D · UniProt O43314
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