MolNFT v1 · #53966 · protein
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with IP5
2XAO · Inositol-pentakisphosphate 2-kinase: “Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from a. thaliana in complex with IP5”. X-ray diffraction, 2 ligands (5MY, ZN), 8 pockets (best druggability 0.85). MolNFT v1 #53966 on GenesisL1: 3D…
- PDB
- 2XAO
- Type
- protein
- Length
- 828 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, ZN
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 404 | 43% helix, 19% strand | Q93YN9 |
| B | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 424 | 45% helix, 18% strand | Q93YN9 |
Ligands and binding sites
- 5MY · Myo-inositol-(1,3,4,5,6)-pentakisphosphate · 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.85 | 0.89 | 98 | 5MY |
| 2 | 490 | 0.82 | 0.89 | 69 | empty |
| 3 | 240 | 0.76 | 0.89 | 44 | 5MY |
| 4 | 164 | 0.65 | 0.86 | 23 | empty |
| 5 | 128 | 0.49 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1214 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2XAO · Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with IP5 · 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 A against A, TM-score 0.99
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 2XAO · PDBe 2XAO · UniProt Q93YN9
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