Research workbench
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with neo-IP5 and ATP
Analyse Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GFH
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol-pentakisphosphate 2-kinase
- EC
- 2.7.1.158
- UniProt
- A0A178UAB5
- Ligands
- K7V, ATP, MG, ZN
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 420 | 41% helix, 17% strand | A0A178UAB5 |
| B | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 410 | 41% helix, 18% strand | A0A178UAB5 |
Ligands and binding sites
- K7V · neo-Inositol pentakisphosphate · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.82 | 0.83 | 106 | K7V, ATP, MG, EDO |
| 2 | 447 | 0.82 | 0.89 | 56 | ATP, MG |
| 3 | 703 | 0.81 | 0.85 | 87 | K7V, EDO |
| 4 | 104 | 0.41 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 760 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6GFH · Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with neo-IP5… · 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 A0A178UAB5
- Elsewhere: RCSB PDB 6GFH · PDBe 6GFH · UniProt A0A178UAB5
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