MolNFT v1 · #170540 · protein
Crystal structure of STK4 (MST1) in complex with compound 6
6YAT · SERINE/THREONINE-protein kinase 4: “Crystal structure of STK4 (MST1) in complex with compound 6”. X-ray diffraction, 2 ligands (OJ5, 3FX), 4 pockets (best druggability 0.70). MolNFT v1 #170540 on GenesisL1: 3D structure, binding…
- PDB
- 6YAT
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase 4
- EC
- 2.7.11.1
- UniProt
- Q13043
- Ligands
- OJ5, 3FX
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase 4 (EC 2.7.11.1) | protein | 291 | 40% helix, 19% strand | Q13043 |
| B | SERINE/THREONINE-protein kinase 4 (EC 2.7.11.1) | protein | 276 | 40% helix, 20% strand | Q13043 |
Ligands and binding sites
- OJ5 · 4-[5-(3-chlorophenyl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]morpholine · ligand · 2 copies · chains A, B
- 3FX · (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid · ligand · chains A
- GOL · Glycerol · additive · 7 copies · chains A
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 | 662 | 0.70 | 0.78 | 76 | OJ5 |
| 2 | 275 | 0.67 | 0.83 | 40 | OJ5 |
| 3 | 491 | 0.66 | 0.78 | 59 | empty |
| 4 | 52 | 0.26 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 796 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6YAT · Crystal structure of STK4 (MST1) in complex with compound 6 · the same entry in another collection · chain A against A, TM-score 1.00
- Q13043 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase 4 (Q13043) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q13043
- Elsewhere: RCSB PDB 6YAT · PDBe 6YAT · UniProt Q13043
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