MolNFT v1 · #144951 · protein
AMP-activated protein kinase bound to pharmacological activator R734
6C9J · 5'-AMP-activated protein kinase catalytic subunit alpha-1: “AMP-activated protein kinase bound to pharmacological activator R734”. X-ray diffraction, 3 ligands (R34, STU, AMP), 13 pockets (best druggability 0.83). MolNFT v1 #144951…
- PDB
- 6C9J
- Type
- protein
- Length
- 860 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-AMP-activated protein kinase catalytic subunit alpha-1; 5'-AMP-activated protein…
- EC
- 2.7.11.1, 2.7.11.27, 2.7.11.31, 2.7.11.26
- UniProt
- Q13131, Q9Y478, P54619
- Ligands
- R34, STU, AMP
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-AMP-activated protein kinase catalytic subunit alpha-1 (EC 2.7.11.1, 2.7.11.27, 2.7.11.31, 2.7.11.26) | protein | 386 | 36% helix, 23% strand | Q13131 |
| B | 5'-AMP-activated protein kinase subunit beta-1 | protein | 174 | 11% helix, 44% strand | Q9Y478 |
| C | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 300 | 42% helix, 23% strand | P54619 |
Ligands and binding sites
- R34 · 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide · ligand · chains A, B
- STU · Staurosporine · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.83 | 0.85 | 84 | AMP |
| 2 | 178 | 0.76 | 0.92 | 28 | empty |
| 3 | 233 | 0.67 | 0.84 | 29 | STU |
| 4 | 356 | 0.66 | 0.80 | 36 | empty |
| 5 | 455 | 0.63 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3701 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1212 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1102 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6C9J · AMP-activated protein kinase bound to pharmacological activator R734 · the same entry in another collection · chain A against A, TM-score 1.00
- Q13131 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9Y478 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta-1… · a predicted model of the same protein · chain B against A, TM-score 0.97
- P54619 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit gamma-1… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q13131
- Every structure of UniProt Q9Y478
- Every structure of UniProt P54619
- Elsewhere: RCSB PDB 6C9J · PDBe 6C9J · UniProt Q13131 · UniProt Q9Y478 · UniProt P54619
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