3NMD Transferase date Jun 22, 2010
title Crystal Structure Of The Leucine Zipper Domain Of Cgmp Depen Protein Kinase I Beta
authors C.Kim, D.E.Casteel, E.V.Smith-Nguyen, B.Sankaran, Berkeley Struc Genomics Center (Bsgc)
compound source
Molecule: Cgmp Dependent Protein Kinase
Chain: A, B, C, D, E
Fragment: Dimerization Docking Domain, Unp Residues 4-55
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prkg1
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
symmetry Space Group: C 2 2 21
R_factor 0.195 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.774 77.312 148.616 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.27 Å
ligand GOL, HEZ, MSE enzyme
Primary referenceA crystal structure of the cyclic GMP-dependent protein kinase I{beta} dimerization/docking domain reveals molecular details of isoform-specific anchoring., Casteel DE, Smith-Nguyen EV, Sankaran B, Roh SH, Pilz RB, Kim C, J Biol Chem. 2010 Oct 22;285(43):32684-8. Epub 2010 Sep 8. PMID:20826808
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (3nmd.pdb1.gz) 37 Kb
  • Biological Unit Coordinates (3nmd.pdb2.gz) 39 Kb
  • Biological Unit Coordinates (3nmd.pdb3.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 3NMD
  • CSU: Contacts of Structural Units for 3NMD
  • Structure Factors (334 Kb)
  • Retrieve 3NMD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NMD from S2C, [Save to disk]
  • Re-refined 3nmd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3NMD in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3NMD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3NMD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nmd_D] [3nmd] [3nmd_B] [3nmd_A] [3nmd_C] [3nmd_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3NMD
  • Community annotation for 3NMD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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