Research workbench
Ampk bound to allosteric activator
Analyse Ampk bound to allosteric activator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T5T
- Type
- protein
- Length
- 825 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
- P54645, P80386, P80385
- Ligands
- AMP, STU, 75O, ADP, CL, SO4
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 28% 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 | 369 | 33% helix, 24% strand | P54645 |
| B | 5'-AMP-activated protein kinase subunit beta-1 | protein | 163 | 15% helix, 45% strand | P80386 |
| C | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 293 | 39% helix, 24% strand | P80385 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains C
- STU · Staurosporine · ligand · chains A
- 75O · 6-chloro-5-[6-(dimethylamino)-2-methoxypyridin-3-yl]-1H-indole-3-carboxylic acid · ligand · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains C
- CL · Chloride ion · ion · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.71 | 0.80 | 52 | AMP, ADP |
| 2 | 625 | 0.70 | 0.78 | 58 | AMP, SO4 |
| 3 | 115 | 0.69 | 0.91 | 28 | empty |
| 4 | 226 | 0.65 | 0.83 | 28 | STU |
| 5 | 102 | 0.62 | 0.88 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2894 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1068 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 429 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- P54645 · 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
- P80385 · 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 0.99
- P80386 · 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 0.94
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 P54645
- Every structure of UniProt P80386
- Every structure of UniProt P80385
- Elsewhere: RCSB PDB 5T5T · PDBe 5T5T · UniProt P54645 · UniProt P80386 · UniProt P80385
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