Research workbench
The structure of the yeast sr protein kinase, SKY1P, with bound ADP
Analyse The structure of the yeast sr protein kinase, SKY1P, with bound ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q8Y
- Type
- protein
- Length
- 708 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sr protein kinase
- EC
- 2.7.1.-
- UniProt
- Q03656
- Ligands
- ADP, ADE, MG, SO4
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sr protein kinase (EC 2.7.1.-) | protein | 351 | 38% helix, 19% strand | Q03656 |
| B | Sr protein kinase (EC 2.7.1.-) | protein | 357 | 41% helix, 18% strand | Q03656 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ADE · Adenine · ligand · chains B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.64 | 0.82 | 29 | MG, ADP |
| 2 | 209 | 0.55 | 0.78 | 22 | ADE |
| 3 | 158 | 0.50 | 0.78 | 16 | empty |
| 4 | 65 | 0.50 | 0.85 | 21 | empty |
| 5 | 74 | 0.42 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 607 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1Q8Y · The structure of the yeast SR protein kinase, Sky1p, with bound ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q03656 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase SKY1 (Q03656) · 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 Q03656
- Elsewhere: RCSB PDB 1Q8Y · PDBe 1Q8Y · UniProt Q03656
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