MolNFT v1 · #25674 · protein
Human inositol (1,4,5)-trisphosphate 3-kinase complexed with MN2+/ADP/INS(1,3,4,5)P4
1W2D · Inositol-trisphosphate 3-kinase a: “Human inositol (1,4,5)-trisphosphate 3-kinase complexed with MN2+/ADP/INS(1,3,4,5)P4”. X-ray diffraction, 4 ligands (ADP, 4IP, MN), 4 pockets (best druggability 0.66). MolNFT v1 #25674 on…
- PDB
- 1W2D
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol-trisphosphate 3-kinase a
- EC
- 2.1.7.127
- UniProt
- P23677
- Ligands
- ADP, 4IP, MN, SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-trisphosphate 3-kinase a (EC 2.1.7.127) | protein | 265 | 40% helix, 22% strand | P23677 |
| B | Inositol-trisphosphate 3-kinase a (EC 2.1.7.127) | protein | 250 | 38% helix, 23% strand | P23677 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- 4IP · Inositol-(1,3,4,5)-tetrakisphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.66 | 0.78 | 52 | SO4 |
| 2 | 242 | 0.56 | 0.78 | 41 | ADP, MN |
| 3 | 196 | 0.53 | 0.78 | 29 | ADP, MN |
| 4 | 71 | 0.37 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 858 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1W2D · Human Inositol (1,4,5)-trisphosphate 3-kinase complexed with Mn2+/ADP/Ins(1,3,4,5)P4 · the same entry in another collection · chain A against A, TM-score 1.00
- P23677 · AlphaFold monomer V2.0 prediction for inositol-trisphosphate 3-kinase a (P23677) · a predicted model of the same protein · 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 P23677
- Elsewhere: RCSB PDB 1W2D · PDBe 1W2D · UniProt P23677
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.