1CTP

STRUCTURE OF THE MAMMALIAN CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE AND AN INHIBITOR PEPTIDE DISPLAYS AN OPEN CONFORMATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 
    0.200 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation.

Karlsson, R.Zheng, J.Xuong, N.Taylor, S.S.Sowadski, J.M.

(1993) Acta Crystallogr D Biol Crystallogr 49: 381-388

  • DOI: https://doi.org/10.1107/S0907444993002306
  • Primary Citation of Related Structures:  
    1CTP

  • PubMed Abstract: 

    The crystal structure of a binary complex of the porcine heart catalytic (C) subunit of cAMP-dependent protein kinase (space group P4(1)32; a = 171.5 A) complexed with a di-iodinated peptide inhibitor, PKI(5-24), has been solved and refined to 2.9 A resolution with an overall R of 21.1%. The r.m.s. deviations from ideal bond lengths and angles are 0.022 A and 4.3 degrees. A single isotropic B of 17 A(2) was used for all atoms. The structure solution was carried out initially by molecular replacement of electron density followed by refinement against atomic coordinates from orthorhombic crystals of a binary complex of the mouse recombinant enzyme previously described [Knighton, Zheng, Ten Eyck, Ashford, Xuong, Taylor & Sowadski (1991). Science, 253, 407-414]. The most striking difference between the two crystal structures is a large displacement of the small lobe of the enzyme. In the cubic crystal, the beta-sheet of the small lobe is rotated by 15 degrees and translated by 1.9 A with respect to the orthorhombic crystal. Possible explanations for why this binary complex crystallized in an open conformation in contrast to a similar binary complex of the recombinant enzyme are discussed. This study demonstrates that considerable information about parts of a crystal structure can be obtained without a complete crystal structure analysis. Specifically, the six rigid-group parameters of a poly alanine model of the beta-structure were obtained satisfactorily from a crystal structure by refinement of difference Fourier coefficients based on an approximate partial structure model.


  • Organizational Affiliation

    Department of Medicine, University of California, San Diego, La Jolla 92093-0654, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-DEPENDENT PROTEIN KINASEA [auth E]350Sus scrofaMutation(s): 0 
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
UniProt
Find proteins for P36887 (Sus scrofa)
Explore P36887 
Go to UniProtKB:  P36887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36887
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase inhibitor, alpha formB [auth I]20Homo sapiensMutation(s): 0 
UniProt
Find proteins for P61926 (Oryctolagus cuniculus)
Explore P61926 
Go to UniProtKB:  P61926
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61926
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download Ideal Coordinates CCD File 
C [auth E]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A [auth E]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
TYI
Query on TYI
B [auth I]L-PEPTIDE LINKINGC9 H9 I2 N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work:  0.200 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.5α = 90
b = 171.5β = 90
c = 171.5γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MYRClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-07-18
    Changes: Source and taxonomy
  • Version 1.4: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.5: 2024-10-30
    Changes: Structure summary