6ESA | pdb_00006esa

Crystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp120 and AMP

• PDB DOI: https://doi.org/10.2210/pdb6ESA/pdb

• Classification: TRANSFERASE
• Organism(s): Cricetulus griseus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-10-19 Released: 2018-10-31 
• Deposition Author(s): Mueller, J.M., Heine, A., Klebe, G.
• Funding Organization(s): Loewe Corporation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Literature

Conceptional Design of Self-Assembling Bisubstrate-like Inhibitors of Protein Kinase A Resulting in a Boronic Acid Glutamate Linkage

Mueller, J.M., Kirschner, R., Geyer, A., Klebe, G.

(2019) ACS Omega 

• DOI: https://doi.org/10.1021/acsomega.8b02364

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: 43.87 kDa 
• Atom Count: 3,405 
• Modeled Residue Count: 359 
• Deposited Residue Count: 371 
• 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	B [auth E]	18	Cricetulus griseus	Mutation(s): 0
UniProt
Find proteins for G3HK48 (Cricetulus griseus) Explore G3HK48  Go to UniProtKB:  G3HK48

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
RIP	F [auth E]	beta-D-ribopyranose C5 H10 O5 SRBFZHDQGSBBOR-TXICZTDVSA-N
MPD	D [auth A], E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-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: 1.31 Å
• R-Value Free:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.939	α = 90
b = 80.327	β = 90
c = 85.002	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Mueller, J.M., Heine, A., Klebe, G.

---

Funding Organization	Location	Grant Number
Loewe Corporation	Germany	--

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2019-05-15
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary