5N3G | pdb_00005n3g

cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule (R)-1,4-oxazepan-6-ol

• PDB DOI: https://doi.org/10.2210/pdb5N3G/pdb

• Classification: TRANSFERASE
• Organism(s): Cricetulus griseus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-08 Released: 2018-02-28 
• Deposition Author(s): Siefker, C., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.157 (Depositor), 0.158 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

A crystallographic fragment study with cAMP-dependent protein kinase A

Siefker, C., Heine, A., Klebe, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.66 kDa 
• Atom Count: 3,360 
• Modeled Residue Count: 340 
• Deposited Residue Count: 353 
• Unique protein chains: 1

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	D [auth A], E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
8KB	B [auth A], C [auth A]	(6~{R})-1,4-oxazepan-6-ol C5 H11 N O2 AJQUDIYIICBQDR-RXMQYKEDSA-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: 1.16 Å
• R-Value Free:  0.157 (Depositor), 0.158 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.223	α = 90
b = 71.925	β = 90
c = 97.733	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Siefker, C., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary