2YZA Transferase date May 04, 2007
title Crystal Structure Of Kinase Domain Of Human 5'-Amp-Activated Kinase Alpha-2 Subunit Mutant (T172d)
authors S.Saijo, T.Takagi, S.Yoshikawa, S.Kishishita, M.Shirouzu, S.Yokoy Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: 5'-Amp-Activated Protein Kinase Catalytic Subunit
Chain: A
Fragment: Kinase Domain
Synonym: 5'-Amp-Activated Protein Kinase Alpha-2 Subunit, A Chain;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prkaa2, Ampk, Ampk2
Expression_system: Cell-Free Protein Synthesis
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Px060824-01
symmetry Space Group: P 1 21 1
R_factor 0.227 R_Free 0.308
length a length b length c angle alpha angle beta angle gamma
39.187 67.336 50.651 90.00 91.26 90.00
method X-Ray Diffractionresolution 3.02 Å
enzyme Transferase E.C. BRENDA

Primary referenceStructural basis for compound C inhibition of the human AMP-activated protein kinase alpha2 subunit kinase domain., Handa N, Takagi T, Saijo S, Kishishita S, Takaya D, Toyama M, Terada T, Shirouzu M, Suzuki A, Lee S, Yamauchi T, Okada-Iwabu M, Iwabu M, Kadowaki T, Minokoshi Y, Yokoyama S, Acta Crystallogr D Biol Crystallogr. 2011 May;67(Pt 5):480-7. Epub 2011 Apr 14. PMID:21543851
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (2yza.pdb1.gz) 41 Kb
  • CSU: Contacts of Structural Units for 2YZA
  • Likely Quarternary Molecular Structure file(s) for 2YZA
  • Structure Factors (39 Kb)
  • Retrieve 2YZA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YZA from S2C, [Save to disk]
  • Re-refined 2yza structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YZA 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 2YZA
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2YZA, from MSDmotif at EBI
  • Fold representative 2yza from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yza_A] [2yza]
  • SWISS-PROT database: [P54646]
  • Domain organization of [AAPK2_HUMAN] by SWISSPFAM
  • Domain found in 2YZA: [S_TKc ] by SMART
  • Other resources with information on 2YZA
  • Community annotation for 2YZA 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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