› 6yqi

X-ray diffraction
1.42Å resolution

Crystal structure of cAMP-dependent Protein Kinase (PKA) in complex with long-chain Fasudil-derivative N-[2-(propylamino)ethyl]isoquinoline-5-sulfonamide (soaked)

Released:
DOI: 10.2210/pdb6yqi/pdb
PDB entry 6yqi coloured by chain, front view.
PDB entry 6yqi coloured by chain, side view.
PDB entry 6yqi coloured by chain, top view.
Source organisms:
Primary publication:
Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses.
Wienen-Schmidt B, Oebbeke M, Ngo K, Heine A, Klebe G
ChemMedChem 16 292-300 (2021)
PMID: 33029876

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150426 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
cAMP-dependent protein kinase catalytic subunit alpha Chain: A
Molecule details ›
Chain: A
Length: 353 amino acids
Theoretical weight: 41.19 KDa
Source organism: Cricetulus griseus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P25321 (Residues: 1-351; Coverage: 100%)
Gene name: PRKACA
Sequence domains: Protein kinase domain
cAMP-dependent protein kinase inhibitor alpha Chain: B
Molecule details ›
Chain: B
Length: 19 amino acids
Theoretical weight: 1.99 KDa
Source organism: Mus musculus
Expression system: Not provided
UniProt:
  • Canonical: P63248 (Residues: 12-30; Coverage: 25%)
Gene name: Pkia

Ligands and Environments

1 bound ligand:
Ligand 6TV 1 x 6TV
2 modified residues:
Ligand SEP 3 x SEP
Ligand TPO 1 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P212121
Unit cell:
a: 58.107Å b: 72.482Å c: 108.739Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.155 0.154 0.18
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Towards design of drugs and delivery systems with the Martini coarse-grained model.
Kjølbye et al. (2022)
1 more

1 mention without citation

Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses.
Wienen-Schmidt et al. (2021)