Research workbench
Crystal structure of the catalytic domain of PPIP5K2 in complex with amppnp and 2,5-di-O-bn-INSP4
Analyse Crystal structure of the catalytic domain of PPIP5K2 in complex with amppnp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NZO
- 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
- ANP, 2OV, MG
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 26% 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 | 26% helix, 31% strand | O43314 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- 2OV · (1R,2R,3r,4S,5S,6s)-3,6-bis(benzyloxy)cyclohexane-1,2,4,5-tetrayl tetrakis[dihydrogen (phosphate)] · 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
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 | 916 | 0.80 | 0.82 | 71 | ANP, MG |
| 2 | 67 | 0.32 | 0.75 | 19 | empty |
Compared structures
- 4NZO · Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and… · 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 4NZO · PDBe 4NZO · UniProt O43314
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