3NMD

Crystal structure of the leucine zipper domain of cGMP dependent protein kinase I beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A crystal structure of the cyclic GMP-dependent protein kinase I{beta} dimerization/docking domain reveals molecular details of isoform-specific anchoring.

Casteel, D.E.Smith-Nguyen, E.V.Sankaran, B.Roh, S.H.Pilz, R.B.Kim, C.

(2010) J Biol Chem 285: 32684-32688

  • DOI: https://doi.org/10.1074/jbc.C110.161430
  • Primary Citation of Related Structures:  
    3NMD

  • PubMed Abstract: 

    Cyclic GMP-dependent protein kinase (PKG) is a key mediator of the nitric oxide/cGMP signaling pathway and plays a central role in regulating cardiovascular and neuronal functions. The N-terminal ∼50 amino acids of the kinase are required for homodimerization and association with isoform-specific PKG-anchoring proteins (GKAPs), which target the kinase to specific substrates. To understand the molecular details of PKG dimerization and gain insight into its association with GKAPs, we solved a crystal structure of the PKG Iβ dimerization/docking domain. Our structure provides molecular details of this unique leucine/isoleucine zipper, revealing specific hydrophobic and ionic interactions that mediate dimerization and demonstrating the topology of the GKAP interaction surface.


  • Organizational Affiliation

    From the Department of Medicine and Cancer Center, San Diego, La Jolla, California 92093.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP Dependent PRotein Kinase
A, B, C, D, E
72Homo sapiensMutation(s): 1 
Gene Names: PRKG1
EC: 2.7.11.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q13976 (Homo sapiens)
Explore Q13976 
Go to UniProtKB:  Q13976
PHAROS:  Q13976
GTEx:  ENSG00000185532 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13976
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
F [auth A]
G [auth C]
H [auth C]
I [auth C]
J [auth D]
F [auth A],
G [auth C],
H [auth C],
I [auth C],
J [auth D],
K [auth D],
M [auth E]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.774α = 90
b = 77.312β = 90
c = 148.616γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-10-30
    Changes: Structure summary