Research workbench
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with ADP and IP5.
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
- 3UDT
- Type
- protein
- Length
- 770 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
- Q93YN9
- Ligands
- 5MY, ADP, MG, ZN
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 385 | 42% helix, 17% strand | Q93YN9 |
| B | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 385 | 45% helix, 17% strand | Q93YN9 |
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 · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.85 | 0.86 | 122 | 5MY, ADP, MG |
| 2 | 950 | 0.84 | 0.85 | 111 | 5MY, ADP, MG |
| 3 | 64 | 0.68 | 0.95 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 714 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3UDT · Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q93YN9 · AlphaFold monomer V2.0 prediction for inositol-pentakisphosphate 2-kinase (Q93YN9) · a predicted model of the same protein · chain B 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 Q93YN9
- Elsewhere: RCSB PDB 3UDT · PDBe 3UDT · UniProt Q93YN9
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