Research workbench
The apoenzyme structure of the yeast sr protein kinase, SKY1P
Analyse The apoenzyme structure of the yeast sr protein kinase, SKY1P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q8Z
- Type
- protein
- Length
- 718 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
- SO4
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sr protein kinase (EC 2.7.1.-) | protein | 354 | 38% helix, 20% strand | Q03656 |
| B | Sr protein kinase (EC 2.7.1.-) | protein | 364 | 38% helix, 19% strand | Q03656 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- MOH · Methanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.65 | 0.81 | 33 | empty |
| 2 | 298 | 0.64 | 0.80 | 28 | empty |
| 3 | 179 | 0.53 | 0.78 | 23 | empty |
| 4 | 80 | 0.45 | 0.80 | 13 | empty |
| 5 | 117 | 0.41 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 580 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1Q8Z · The apoenzyme structure of the yeast SR protein kinase, Sky1p · the same entry in another collection · chain B against B, 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 1Q8Z · PDBe 1Q8Z · UniProt Q03656
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