Research workbench
Co-crystal structure of an ampk core with ATP
Analyse Co-crystal structure of an ampk core with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EAK
- Type
- protein
- Length
- 419 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
- ATP, TAM
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 35% 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 | 92 | 35% helix, 38% strand | P54645 |
| B | 5'-AMP-activated protein kinase subunit beta-1 | protein | 42 | 0% helix, 57% strand | P80386 |
| C | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 285 | 41% helix, 23% strand | P80385 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.80 | 0.82 | 88 | ATP, TAM |
| 2 | 145 | 0.61 | 0.84 | 13 | empty |
| 3 | 101 | 0.45 | 0.79 | 27 | empty |
| 4 | 89 | 0.38 | 0.76 | 15 | empty |
| 5 | 82 | 0.37 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1103 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 889 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4EAK · Co-crystal structure of an AMPK core with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.98
- 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
- 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 0.91
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 4EAK · PDBe 4EAK · UniProt P54645 · UniProt P80386 · UniProt P80385
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