Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.62 kDa 
• Atom Count: 5639 
• Residue Count: 644 
• Unique protein chains: 1

3AG9

Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1012

• DOI: 10.2210/pdb3AG9/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-26 Released: 2010-09-01 
• Deposition Author(s): Pflug, A., Lavogina, D., Uri, A., Engh, R.A., Bossemeyer, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

Diversity of bisubstrate binding modes of adenosine analogue-oligoarginine conjugates in protein kinase a and implications for protein substrate interactions.

Pflug, A., Rogozina, J., Lavogina, D., Enkvist, E., Uri, A., Engh, R.A., Bossemeyer, D.

(2010) J Mol Biol 403: 66-77

• PubMed: 20732331 
• DOI: 10.1016/j.jmb.2010.08.028
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Crystal structures of the catalytic subunit α of cAMP-dependent protein kinase (PKAc) with three adenosine analogue-oligoarginine conjugates (ARCs) are presented. The rationally designed ARCs include moieties that, in combination, target both the ATP- and the peptide-substrate-binding sites of PKAc, thereby taking advantage of high-affinity binding interactions offered by the ATP site while utilizing an additional mechanism for target specificity via binding to the peptide substrate site. The crystal structures demonstrate that, in accord with the previously reported bisubstrate character of ARCs, the inhibitors occupy both binding sites of PKAc. Further, they show new binding modes that may also apply to natural protein substrates of PKAc, which have not been revealed by previous crystallographic studies. The crystal structures described here contribute to the understanding of the substrate-binding patterns of PKAc and should also facilitate the design of inhibitors targeting PKAc and related protein kinases.

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Organizational Affiliation: 

German Cancer Research Center, Group of Structural Biochemistry, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
cAMP-dependent protein kinase catalytic subunit alpha	A, B	351	Bos taurus	Mutation(s): 0  Gene Names: PRKACA EC: 2.7.11.11
Find proteins for P00517 (Bos taurus) Explore P00517  Go to UniProtKB:  P00517

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A02	B	(10R,20R,23R)-10-(4-aminobutyl)-1-[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-20,23-bis(3-carbamimidamidopropyl)-1,8,11,18,21-pentaoxo-2,9,12,19,22-pentaazatetracosan-24-amide C40 H70 N18 O9 LIYNJKNSBUCWCZ-SAPGASOESA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000641 (A02)	B	INHIBITOR ARC-1012	N /  Inhibitor		--

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
A02	Ki :  9   nM  PDBBind
A02	Ki:  9   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.68	α = 90
b = 88.04	β = 90
c = 115.07	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-26 
• Released Date: 2010-09-01 
Deposition Author(s): Pflug, A., Lavogina, D., Uri, A., Engh, R.A., Bossemeyer, D.

Revision History 

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other