Research workbench
Structure of human YSK1 (yeast SPS1-STE20-related kinase 1)
Analyse Structure of human YSK1 (yeast SPS1-STE20-related kinase 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XIK
- Type
- protein
- Length
- 289 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE protein kinase 25
- EC
- 2.7.11.1
- UniProt
- O00506
- Ligands
- J60
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE protein kinase 25 (EC 2.7.11.1) | protein | 289 | 40% helix, 19% strand | O00506 |
Ligands and binding sites
- J60 · 5-[(E)-(5-chloro-2-oxo-1,2-dihydro-3H-indol-3-ylidene) methyl]-N-[2-(diethylamino)ethyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.67 | 0.84 | 32 | J60 |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 2XIK · Structure of Human YSK1 (Yeast Sps1-Ste20-related Kinase 1) · the same entry in another collection · chain A against A, TM-score 1.00
- O00506 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase 25 (O00506) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 O00506
- Elsewhere: RCSB PDB 2XIK · PDBe 2XIK · UniProt O00506
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