Research workbench
Human inositol (1,4,5)-trisphosphate 3-kinase substituted with selenomethionine
Analyse Human inositol (1,4,5)-trisphosphate 3-kinase substituted with selenomethionine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W2F
- Type
- protein
- Length
- 548 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
- SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-trisphosphate 3-kinase a (EC 2.1.7.127) | protein | 276 | 40% helix, 22% strand | P23677 |
| B | Inositol-trisphosphate 3-kinase a (EC 2.1.7.127) | protein | 272 | 42% helix, 23% strand | P23677 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.69 | 0.76 | 90 | SO4 |
| 2 | 228 | 0.53 | 0.77 | 31 | empty |
| 3 | 100 | 0.37 | 0.75 | 19 | empty |
| 4 | 89 | 0.33 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 919 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1W2F · Human Inositol (1,4,5)-trisphosphate 3-kinase substituted with selenomethionine · 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 B against A, TM-score 0.97
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 1W2F · PDBe 1W2F · UniProt P23677
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