MolNFT v1 · #188938 · protein
Crystal structure of C-terminal domain of MSK1 in complex with covalently bound pyrrolopyrimidine compound 27 (co-crystal)
7UP8 · Ribosomal protein S6 kinase alpha-5: “Crystal structure of C-terminal domain of MSK1 in complex with covalently bound pyrrolopyrimidine compound 27…”. X-ray diffraction, 1 ligand (O10), 8 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 7UP8
- Type
- protein
- Length
- 553 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein S6 kinase alpha-5
- EC
- 2.7.11.1
- UniProt
- O75582
- Ligands
- O10
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein S6 kinase alpha-5 (EC 2.7.11.1) | protein | 273 | 40% helix, 18% strand | O75582 |
| B | Ribosomal protein S6 kinase alpha-5 (EC 2.7.11.1) | protein | 280 | 41% helix, 18% strand | O75582 |
Ligands and binding sites
- O10 · (5M)-5-(5-bromo-2-chloropyrimidin-4-yl)-5H-pyrrolo[3,2-d]pyrimidine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.67 | 0.80 | 39 | O10 |
| 2 | 406 | 0.67 | 0.79 | 40 | O10 |
| 3 | 80 | 0.50 | 0.83 | 16 | empty |
| 4 | 50 | 0.44 | 0.84 | 19 | empty |
| 5 | 70 | 0.43 | 0.81 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 336 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 7UP8 · Crystal structure of C-terminal Domain of MSK1 in complex with covalently bound… · the same entry in another collection · chain A against A, TM-score 1.00
- O75582 · AlphaFold monomer V2.0 prediction for ribosomal protein S6 kinase alpha-5 (O75582) · 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 O75582
- Elsewhere: RCSB PDB 7UP8 · PDBe 7UP8 · UniProt O75582
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