3POO | pdb_00003poo

human cAMP-dependent protein kinase in complex with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3POO/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-11-23 Released: 2011-11-16 
• Deposition Author(s): Koester, H., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.212 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

fragment based drug design on PKA

Koester, H., Craan, T., Heine, A., Klebe, G.

To be published.

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: 43.44 kDa 
• Atom Count: 3,127 
• Modeled Residue Count: 352 
• 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	351	Homo sapiens	Mutation(s): 0  Gene Names: PKACA, PRKACA EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens) Explore P17612  Go to UniProtKB:  P17612
PHAROS:  P17612 GTEx:  ENSG00000072062

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B	20	Homo sapiens	Mutation(s): 0  Gene Names: PKIA
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S69	C [auth A]	N'-[(E)-(2,4-dihydroxy-6-methylphenyl)methylidene]-2-(3-methoxyphenyl)acetohydrazide C17 H18 N2 O4 BVOFXQXPHVPLFB-VCHYOVAHSA-N
BUD	D [auth A]	(2S,3S)-butane-2,3-diol C4 H10 O2 OWBTYPJTUOEWEK-IMJSIDKUSA-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: 1.60 Å
• R-Value Free:  0.212 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.87	α = 90
b = 74.94	β = 90
c = 79.7	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-16 
Deposition Author(s): Koester, H., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2011-11-16
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary