Research workbench
Co-crystal of ampk core with AMP soaked with ATP
Analyse Co-crystal of ampk core with AMP soaked with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EAJ
- Type
- protein
- Length
- 440 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, O43741, P80385
- Ligands
- ATP, AMP
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 30% 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 | 100 | 30% helix, 37% strand | P54645 |
| B | 5'-AMP-activated protein kinase subunit beta-2 | protein | 51 | 0% helix, 55% strand | O43741 |
| C | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 289 | 39% helix, 24% strand | P80385 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C
- AMP · Adenosine monophosphate · ligand · chains C
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 | 1050 | 0.77 | 0.79 | 96 | ATP, AMP |
| 2 | 80 | 0.54 | 0.86 | 23 | empty |
| 3 | 59 | 0.52 | 0.87 | 16 | empty |
| 4 | 107 | 0.50 | 0.81 | 14 | empty |
| 5 | 119 | 0.44 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1513 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 888 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 447 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4EAJ · Co-crystal of AMPK core with AMP soaked with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.96
- 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 0.94
- O43741 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta-2… · a predicted model of the same protein · chain B against A, TM-score 0.87
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 O43741
- Every structure of UniProt P80385
- Elsewhere: RCSB PDB 4EAJ · PDBe 4EAJ · UniProt P54645 · UniProt O43741 · UniProt P80385
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.