Research workbench
Structure of the regulatory fragment of mammalian ampk in complex with coumarin ADP
Analyse Structure of the regulatory fragment of mammalian ampk in complex with coumarin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YA3
- Type
- protein
- Length
- 470 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
- UniProt
- P54645, O43741, P80385
- Ligands
- J7V, AMP
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-AMP-activated protein kinase catalytic subunit alpha-1 (EC 2.7.11.1) | protein | 102 | 29% helix, 39% strand | P54645 |
| B | 5'-AMP-activated protein kinase subunit beta-2 | protein | 68 | 4% helix, 41% strand | O43741 |
| E | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 300 | 42% helix, 23% strand | P80385 |
Ligands and binding sites
- J7V · 3'-(7-diethylaminocoumarin-3-carbonylamino)-3'-deoxy-ADP · ligand · 2 copies · chains E
- AMP · Adenosine monophosphate · ligand · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.76 | 0.78 | 80 | J7V, AMP |
| 2 | 246 | 0.58 | 0.78 | 33 | empty |
| 3 | 219 | 0.56 | 0.79 | 41 | empty |
| 4 | 87 | 0.46 | 0.80 | 16 | empty |
| 5 | 153 | 0.46 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1629 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 946 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 719 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2YA3 · Structure of the regulatory fragment of mammalian ampk in complex with coumarin ADP · 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 E 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 0.90
- 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 0.71
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 2YA3 · PDBe 2YA3 · UniProt P54645 · UniProt O43741 · UniProt P80385
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