5LCT | pdb_00005lct

Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with a R-methyl-piperazine substituted Fasudil-derivative (Ligand 02)

• PDB DOI: https://doi.org/10.2210/pdb5LCT/pdb

• Classification: TRANSFERASE
• Organism(s): Cricetulus griseus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-22 Released: 2018-01-17 
• Deposition Author(s): Wienen-Schmidt, B., Heine, A., Klebe, G.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.174 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with different Fasudil-derivatives

Wienen-Schmidt, B., Jonker, H.R.A., Wulsdorf, T., Gerber, H.-D., Saxena, K., Kudlinzki, D., Sreeramulu, S., Parigi, G., Luchinat, C., Heine, A., Schwalbe, H., Klebe, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.81 kDa 
• Atom Count: 3,491 
• Modeled Residue Count: 373 
• Deposited Residue Count: 373 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	353	Cricetulus griseus	Mutation(s): 0  Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P25321 (Cricetulus griseus) Explore P25321  Go to UniProtKB:  P25321

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens) Explore P61925  Go to UniProtKB:  P61925
PHAROS:  P61925 GTEx:  ENSG00000171033

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6TY	C [auth A]	5-[(2~{R})-2-methylpiperazin-1-yl]sulfonylisoquinoline C14 H17 N3 O2 S BDVFVCGFMNCYPV-LLVKDONJSA-N
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MOH	E [auth A], F [auth A]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.174 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.014	α = 90
b = 73.7	β = 90
c = 109.837	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Wienen-Schmidt, B., Heine, A., Klebe, G.

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Funding Organization	Location	Grant Number
European Research Council	Belgium	268145 - Project Acronym: DrugProfilBind

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary