MolNFT v1 · #105762 · protein
Crystal structure of the phosphorylated human ALPHA1 BETA2 GAMMA1 holo-ampk complex bound to AMP and cyclodextrin
4RER · 5'-AMP-activated protein kinase catalytic subunit alpha-1: “Crystal structure of the phosphorylated human ALPHA1 BETA2 GAMMA1 holo-ampk complex bound to AMP and…”. X-ray diffraction, 3 ligands (AMP, STU, GLC), 14 pockets (best…
- PDB
- 4RER
- Type
- protein
- Length
- 940 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
- Q13131, O43741, P54619
- Ligands
- AMP, STU, GLC
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 23% 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 | 459 | 33% helix, 19% strand | Q13131 |
| B | 5'-AMP-activated protein kinase subunit beta-2 | protein | 181 | 4% helix, 31% strand | O43741 |
| G | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 300 | 37% helix, 23% strand | P54619 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains G, A
- STU · Staurosporine · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 7 copies · chains B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.83 | 0.84 | 84 | AMP |
| 2 | 1170 | 0.78 | 0.80 | 77 | empty |
| 3 | 201 | 0.78 | 0.92 | 38 | empty |
| 4 | 939 | 0.72 | 0.76 | 80 | empty |
| 5 | 600 | 0.71 | 0.79 | 57 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4070 Ų buried · 37 hydrogen bonds · protein-protein
- A–G · 1628 Ų buried · 21 hydrogen bonds · protein-protein
- B–G · 1224 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4RER · Crystal structure of the phosphorylated human alpha1 beta2 gamma1 holo-AMPK complex bound… · the same entry in another collection · chain A against A, TM-score 1.00
- P54619 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit gamma-1… · a predicted model of the same protein · chain G against A, TM-score 0.96
- Q13131 · 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 0.96
- 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 0.84
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 Q13131
- Every structure of UniProt O43741
- Every structure of UniProt P54619
- Elsewhere: RCSB PDB 4RER · PDBe 4RER · UniProt Q13131 · UniProt O43741 · UniProt P54619
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