MolNFT v1 · #53212 · protein
Crystal structure of the human ribosomal protein S6 kinase
2WNT: “Crystal structure of the human ribosomal protein S6 kinase”. X-ray diffraction, 2 ligands (NA, CL), 6 pockets (best druggability 0.64). MolNFT v1 #53212 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WNT
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein S6 kinase
- EC
- 2.7.11.1
- UniProt
- Q15418
- Ligands
- NA, CL
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein S6 kinase (EC 2.7.11.1) | protein | 281 | 43% helix, 19% strand | Q15418 |
| B | Ribosomal protein S6 kinase (EC 2.7.11.1) | protein | 285 | 42% helix, 18% strand | Q15418 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.64 | 0.80 | 37 | empty |
| 2 | 310 | 0.62 | 0.79 | 41 | empty |
| 3 | 188 | 0.50 | 0.76 | 27 | empty |
| 4 | 139 | 0.42 | 0.75 | 17 | empty |
| 5 | 89 | 0.38 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 750 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2WNT · Crystal Structure of the Human Ribosomal protein S6 kinase · the same entry in another collection · chain A against A, TM-score 1.00
- Q15418 · AlphaFold monomer V2.0 prediction for ribosomal protein S6 kinase alpha-1 (Q15418) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q15418
- Elsewhere: RCSB PDB 2WNT · PDBe 2WNT · UniProt Q15418
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