Research workbench
Myo-inositol 3-kinase bound with its products (ADP and 1D-myo-inositol 3-phosphate)
Analyse Myo-inositol 3-kinase bound with its products (ADP and 1D-myo-inositol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XF6
- 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
- LIP, ADP, INS, MG, IOD
- Pockets
- 3 · 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
- LIP · L-myo-inositol-1-phosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 15 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.76 | 0.86 | 50 | LIP, ADP, INS, MG |
| 2 | 313 | 0.75 | 0.87 | 47 | LIP, ADP, INS, MG |
| 3 | 67 | 0.31 | 0.74 | 13 | IOD |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4XF6 · myo-inositol 3-kinase bound with its products (ADP and 1D-myo-inositol 3-phosphate) · 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 4XF6 · PDBe 4XF6 · UniProt Q5JDA3
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