Research workbench
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with myo-IP5 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
- 6FL3
- Type
- protein
- Length
- 845 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
- 5MY, ADP, MG, ZN
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 425 | 41% helix, 18% strand | A0A178UAB5 |
| B | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 420 | 42% helix, 18% strand | A0A178UAB5 |
Ligands and binding sites
- 5MY · Myo-inositol-(1,3,4,5,6)-pentakisphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.86 | 0.88 | 100 | 5MY, ADP, MG, B3P |
| 2 | 992 | 0.82 | 0.83 | 98 | 5MY, ADP, MG |
| 3 | 52 | 0.63 | 0.93 | 15 | empty |
| 4 | 142 | 0.59 | 0.84 | 26 | empty |
| 5 | 355 | 0.59 | 0.76 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 916 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6FL3 · Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with myo-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 6FL3 · PDBe 6FL3 · UniProt A0A178UAB5
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