MolNFT v1 · #127427 · protein
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from M. musculus in complex with ATP and IP5
5MW8 · Inositol-pentakisphosphate 2-kinase: “Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from M. musculus in complex with ATP and IP5”. X-ray diffraction, 4 ligands (ATP, 5MY, MG), 5 pockets (best druggability 0.82). MolNFT v1 #127427 on…
- PDB
- 5MW8
- Type
- protein
- Length
- 414 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol-pentakisphosphate 2-kinase
- EC
- 2.7.1.158
- UniProt
- Q6P1C1
- Ligands
- ATP, 5MY, MG, ZN
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 414 | 43% helix, 14% strand | Q6P1C1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 5MY · Myo-inositol-(1,3,4,5,6)-pentakisphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.82 | 0.83 | 96 | ATP, 5MY, MG |
| 2 | 90 | 0.50 | 0.83 | 19 | empty |
| 3 | 71 | 0.48 | 0.83 | 21 | empty |
| 4 | 73 | 0.44 | 0.81 | 12 | empty |
| 5 | 65 | 0.34 | 0.77 | 20 | empty |
Compared structures
- 5MW8 · INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN COMPLEX WITH ATP and IP5 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6P1C1 · AlphaFold monomer V2.0 prediction for inositol-pentakisphosphate 2-kinase (Q6P1C1) · 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 Q6P1C1
- Elsewhere: RCSB PDB 5MW8 · PDBe 5MW8 · UniProt Q6P1C1
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