MolNFT v1 · #55107 · protein
Structure of the regulatory fragment of mammalian ampk in complex with coumarin ADP
2YA3 · 5'-AMP-activated protein kinase catalytic subunit alpha-1: “Structure of the regulatory fragment of mammalian ampk in complex with coumarin ADP”. X-ray diffraction, 2 ligands (J7V, AMP), 6 pockets (best druggability 0.76). MolNFT v1…
- 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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