Research workbench
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with D-chiro-IP6 and ADP
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
- 6GFG
- Type
- protein
- Length
- 840 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
- KGN, ADP, MG, ZN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 420 | 41% helix, 16% strand | A0A178UAB5 |
Ligands and binding sites
- KGN · D-chiro inositol hexakisphosphate · ligand · 2 copies · chains B, A
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 4 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.82 | 0.88 | 72 | ADP, MG |
| 2 | 981 | 0.82 | 0.83 | 86 | KGN, ADP, MG |
| 3 | 216 | 0.71 | 0.87 | 38 | KGN |
| 4 | 87 | 0.53 | 0.85 | 20 | MG |
| 5 | 72 | 0.49 | 0.83 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 796 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6GFG · Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with… · the same entry in another collection · chain B against B, 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 6GFG · PDBe 6GFG · UniProt A0A178UAB5
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