MolNFT v1 · #53963 · protein
Lead derivative of inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with ADP and IP6.
2XAL · Inositol-pentakisphosphate 2-kinase: “Lead derivative of inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with ADP and IP6.”. X-ray diffraction, 4 ligands (IHP, ADP, PB), 9 pockets (best druggability 0.87).…
- PDB
- 2XAL
- 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
- Q93YN9
- Ligands
- IHP, ADP, PB, ZN
- Pockets
- 9 · best druggability 0.87
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 | 420 | 41% helix, 18% strand | Q93YN9 |
| B | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 425 | 43% helix, 18% strand | Q93YN9 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- PB · Lead (II) ion · metal · 4 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.87 | 0.89 | 100 | IHP, PB, ADP |
| 2 | 493 | 0.81 | 0.88 | 65 | empty |
| 3 | 244 | 0.77 | 0.91 | 35 | PB, ADP |
| 4 | 398 | 0.67 | 0.80 | 40 | empty |
| 5 | 129 | 0.50 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1204 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2XAL · Lead derivative of Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in… · the same entry in another collection · chain B against B, 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 2XAL · PDBe 2XAL · UniProt Q93YN9
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