2CPK | pdb_00002cpk

CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF CYCLIC ADENOSINE MONOPHOSPHATE-DEPENDENT PROTEIN KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 
    0.180 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase.

Knighton, D.R.Zheng, J.H.Ten Eyck, L.F.Ashford, V.A.Xuong, N.H.Taylor, S.S.Sowadski, J.M.

(1991) Science 253: 407-414

  • DOI: https://doi.org/10.1126/science.1862342
  • Primary Citation Related Structures: 
    2CPK

  • PubMed Abstract: 

    The crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase complexed with a 20-amino acid substrate analog inhibitor has been solved and partially refined at 2.7 A resolution to an R factor of 0.212. The magnesium adenosine triphosphate (MgATP) binding site was located by difference Fourier synthesis. The enzyme structure is bilobal with a deep cleft between the lobes. The cleft is filled by MgATP and a portion of the inhibitor peptide. The smaller lobe, consisting mostly of amino-terminal sequence, is associated with nucleotide binding, and its largely antiparallel beta sheet architecture constitutes an unusual nucleotide binding motif. The larger lobe is dominated by helical structure with a single beta sheet at the domain interface. This lobe is primarily involved in peptide binding and catalysis. Residues 40 through 280 constitute a conserved catalytic core that is shared by more than 100 protein kinases. Most of the invariant amino acids in this conserved catalytic core are clustered at the sites of nucleotide binding and catalysis.


  • Organizational Affiliation
    • Department of Chemistry, University of California, San Diego, La Jolla 92093-0654.

Macromolecule Content 

  • Total Structure Weight: 42.96 kDa 
  • Atom Count: 2,822 
  • Modeled Residue Count: 356 
  • Deposited Residue Count: 370 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cAMP-DEPENDENT PROTEIN KINASE, CATALYTIC SUBUNITA [auth E]350Mus musculusMutation(s): 0 
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
UniProt
Find proteins for P05132 (Mus musculus)
Explore P05132 
Go to UniProtKB:  P05132
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05132
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PEPTIDE INHIBITOR 20-MERB [auth I]20Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P63248 (Mus musculus)
Explore P63248 
Go to UniProtKB:  P63248
IMPC:  MGI:104747
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63248
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A [auth E]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A [auth E]L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work:  0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.62α = 90
b = 76.52β = 90
c = 80.14γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-01-15
    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: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-10-23
    Changes: Structure summary