MolNFT v1 · #69330 · protein
Crystal structure of the C-terminal kinase domain of MSK1 in complex with AMP-pnp
3KN5 · Ribosomal protein S6 kinase alpha-5: “Crystal structure of the C-terminal kinase domain of MSK1 in complex with AMP-pnp”. X-ray diffraction, 1 ligand (ANP), 7 pockets (best druggability 0.67). MolNFT v1 #69330 on GenesisL1: 3D…
- PDB
- 3KN5
- Type
- protein
- Length
- 571 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
- ANP
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein S6 kinase alpha-5 (EC 2.7.11.1) | protein | 282 | 41% helix, 17% strand | O75582 |
| B | Ribosomal protein S6 kinase alpha-5 (EC 2.7.11.1) | protein | 289 | 42% helix, 17% strand | O75582 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.67 | 0.79 | 51 | ANP |
| 2 | 312 | 0.65 | 0.80 | 34 | ANP |
| 3 | 209 | 0.59 | 0.81 | 30 | empty |
| 4 | 53 | 0.52 | 0.87 | 16 | empty |
| 5 | 61 | 0.49 | 0.85 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 307 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3KN5 · Crystal structure of the C-terminal kinase domain of msk1 in complex with AMP-PNP · 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 0.93
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 O75582
- Elsewhere: RCSB PDB 3KN5 · PDBe 3KN5 · UniProt O75582
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.