MolNFT v1 · #144947 · protein
AMP-activated protein kinase bound to pharmacological activator R734
6C9F · 5'-AMP-activated protein kinase catalytic subunit alpha-1…: “AMP-activated protein kinase bound to pharmacological activator R734”. X-ray diffraction, 3 ligands (AMP, R34, STU), 9 pockets (best druggability 0.81). MolNFT v1 #144947…
- PDB
- 6C9F
- Type
- protein
- Length
- 849 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
- AMP, R34, STU
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-AMP-activated protein kinase catalytic subunit alpha-1, 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 | 373 | 35% helix, 24% strand | Q13131 |
| B | 5'-AMP-activated protein kinase subunit beta-1 | protein | 176 | 9% helix, 44% strand | Q9Y478 |
| C | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 300 | 40% helix, 22% strand | P54619 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains C
- 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.81 | 0.82 | 93 | AMP |
| 2 | 333 | 0.67 | 0.81 | 44 | STU |
| 3 | 448 | 0.64 | 0.77 | 33 | empty |
| 4 | 217 | 0.62 | 0.82 | 22 | R34 |
| 5 | 257 | 0.58 | 0.78 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3520 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1176 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 489 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6C9F · 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
- 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
- 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 0.96
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 Q13131
- Every structure of UniProt Q9Y478
- Every structure of UniProt P54619
- Elsewhere: RCSB PDB 6C9F · PDBe 6C9F · UniProt Q13131 · UniProt Q9Y478 · UniProt P54619
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