MolNFT v1 · #53969 · protein
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with IP6.
2XAR · Inositol-pentakisphosphate 2-kinase: “Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with IP6.”. X-ray diffraction, 2 ligands (IHP, ZN), 7 pockets (best druggability 0.87). MolNFT v1 #53969 on GenesisL1…
- PDB
- 2XAR
- Type
- protein
- Length
- 841 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
- IHP, ZN
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 417 | 43% helix, 18% strand | Q93YN9 |
| B | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 424 | 43% helix, 18% strand | Q93YN9 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.87 | 0.89 | 100 | IHP |
| 2 | 843 | 0.82 | 0.84 | 83 | IHP |
| 3 | 287 | 0.74 | 0.87 | 41 | empty |
| 4 | 368 | 0.67 | 0.81 | 35 | empty |
| 5 | 83 | 0.50 | 0.83 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1226 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2XAR · Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with IP6. · 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 0.98
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 2XAR · PDBe 2XAR · UniProt Q93YN9
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