MolNFT v1 · #40084 · protein
Crystal structure of inositol phosphate multikinase IPK2 in complex with ADP and MN2+ from S. cerevisiae
2IF8 · Inositol polyphosphate multikinase: “Crystal structure of inositol phosphate multikinase IPK2 in complex with ADP and MN2+ from S. cerevisiae”. X-ray diffraction, 3 ligands (ADP, MN, CA), 7 pockets (best druggability 0.49). MolNFT…
- PDB
- 2IF8
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol polyphosphate multikinase
- EC
- 2.7.1.151
- UniProt
- P07250
- Ligands
- ADP, MN, CA
- Pockets
- 7 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol polyphosphate multikinase (EC 2.7.1.151) | protein | 255 | 39% helix, 23% strand | P07250 |
| B | Inositol polyphosphate multikinase (EC 2.7.1.151) | protein | 256 | 38% helix, 23% strand | P07250 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.49 | 0.79 | 18 | empty |
| 2 | 185 | 0.49 | 0.76 | 24 | empty |
| 3 | 199 | 0.48 | 0.75 | 28 | empty |
| 4 | 167 | 0.47 | 0.75 | 23 | ADP |
| 5 | 73 | 0.41 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 819 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2IF8 · Crystal structure of Inositol Phosphate Multikinase Ipk2 in complex with ADP and Mn2+… · the same entry in another collection · chain A against A, TM-score 1.00
- P07250 · AlphaFold monomer V2.0 prediction for inositol polyphosphate multikinase (P07250) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P07250
- Elsewhere: RCSB PDB 2IF8 · PDBe 2IF8 · UniProt P07250
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