Research workbench
Structure of ampk in complex with staurosporine inhibitor and in the absence of a synthetic activator
Analyse Structure of ampk in complex with staurosporine inhibitor and in the absence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QFG
- Type
- protein
- Length
- 814 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
- STU, AMP, CL, SO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 28% 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 | 366 | 34% helix, 25% strand | P54645 |
| B | 5'-AMP-activated protein kinase subunit beta-1 | protein | 161 | 10% helix, 42% strand | P80386 |
| C | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 287 | 42% helix, 24% strand | P80385 |
Ligands and binding sites
- STU · Staurosporine · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains C
- CL · Chloride ion · ion · 3 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.78 | 0.80 | 93 | AMP, SO4 |
| 2 | 374 | 0.69 | 0.81 | 47 | SO4 |
| 3 | 205 | 0.60 | 0.81 | 25 | STU |
| 4 | 313 | 0.56 | 0.76 | 27 | empty |
| 5 | 196 | 0.53 | 0.78 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3120 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1156 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 452 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4QFG · Structure of AMPK in complex with STAUROSPORINE inhibitor and in the absence of a… · 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 0.99
- 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 0.98
- 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 0.92
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 4QFG · PDBe 4QFG · UniProt P54645 · UniProt P80386 · UniProt P80385
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.