3DNE

cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24

• PDB DOI: https://doi.org/10.2210/pdb3DNE/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Bos taurus, Oryctolagus cuniculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-02 Released: 2009-06-23 
• Deposition Author(s): Schiffer, A., Wendt, K.U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.176 
• R-Value Observed: 0.180 

Literature

Crystallography-independent determination of ligand binding modes

Orts, J., Tuma, J., Reese, M., Grimm, S.K., Monecke, P., Bartoschek, S., Schiffer, A., Wendt, K.U., Griesinger, C., Carlomagno, T.

(2008) Angew Chem Int Ed Engl 47: 7736-7740

• PubMed: 18767090 
• DOI: https://doi.org/10.1002/anie.200801792
• Primary Citation of Related Structures:  
  3DND, 3DNE

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Organizational Affiliation: 

Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg, 37077 Göttingen, Germany.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 43.13 kDa 
• Atom Count: 3,313 
• Modelled Residue Count: 358 
• Deposited Residue Count: 370 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	350	Bos taurus	Mutation(s): 0  EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517  Go to UniProtKB:  P00517

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B [auth I]	20	N/A	Mutation(s): 0
UniProt
Find proteins for P61926 (Oryctolagus cuniculus) Explore P61926  Go to UniProtKB:  P61926

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LL1	C [auth A]	3-pyridin-4-yl-1H-indazole C12 H9 N3 MSRXUUDVRNWSTN-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

Binding Affinity Annotations
ID	Source	Binding Affinity
LL1	PDBBind:  3DNE	Ki: 6000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.176 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.841	α = 90
b = 75.438	β = 90
c = 79.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
APRV	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Schiffer, A., Wendt, K.U.

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-10-09
  Changes: Derived calculations
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary