Research workbench
Myo-inositol 3-kinase bound with its substrates (amppcp and myo- inositol)
Analyse Myo-inositol 3-kinase bound with its substrates (amppcp and myo- inositol) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XF7
- Type
- protein
- Length
- 546 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CARBOHYDRATE/PYRIMIDINE kinase, pfkb family
- EC
- 2.7.1.64
- UniProt
- Q5JDA3
- Ligands
- INS, ACP, MG, IOD
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CARBOHYDRATE/PYRIMIDINE kinase, pfkb family (EC 2.7.1.64) | protein | 273 | 30% helix, 31% strand | Q5JDA3 |
Ligands and binding sites
- INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · 2 copies · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 22 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.76 | 0.86 | 55 | INS, ACP, MG, IOD |
| 2 | 443 | 0.74 | 0.84 | 49 | INS, ACP, MG |
| 3 | 83 | 0.35 | 0.75 | 17 | IOD |
| 4 | 73 | 0.32 | 0.74 | 16 | IOD |
Interfaces
1 interface between chains.
- A–B · 649 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4XF7 · myo-inositol 3-kinase bound with its substrates (AMPPCP and myo-inositol) · the same entry in another collection · 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 Q5JDA3
- Elsewhere: RCSB PDB 4XF7 · PDBe 4XF7 · UniProt Q5JDA3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.