2ZYB Transferase date Jan 19, 2009
title Crystal Structure Of Phenylimidazo Pyrazin 2 Bound To The Ki Domain Of Human Lck, (Auto-Phosphorylated On Tyr394)
authors E.Tsuji
compound source
Molecule: Proto-Oncogene Tyrosine-Protein Kinase Lck
Chain: A
Fragment: Unp Residues 225-509
Synonym: Lymphocyte Cell-Specific Protein-Tyrosine Kinase, Lsk, T Cell-Specific Protein-Tyrosine Kinase;
Ec: 2.7.10.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lck
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-19b
symmetry Space Group: P 21 21 21
R_factor 0.171 R_Free 0.291
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.150 73.973 92.857 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.55 Å
ligand KSL, PTR, SO4 BindingDB enzyme Transferase E.C.2.7.10.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe importance of CH/pi hydrogen bonds in rational drug design: An ab initio fragment molecular orbital study to leukocyte-specific protein tyrosine (LCK) kinase., Ozawa T, Tsuji E, Ozawa M, Handa C, Mukaiyama H, Nishimura T, Kobayashi S, Okazaki K, Bioorg Med Chem. 2008 Dec 15;16(24):10311-8. Epub 2008 Oct 22. PMID:18977146
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (2zyb.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 2ZYB
  • CSU: Contacts of Structural Units for 2ZYB
  • Likely Quarternary Molecular Structure file(s) for 2ZYB
  • Structure Factors (75 Kb)
  • Retrieve 2ZYB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZYB from S2C, [Save to disk]
  • Re-refined 2zyb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ZYB 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 2ZYB
  • 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 2ZYB, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2zyb_A] [2zyb]
  • SWISS-PROT database: [P06239]
  • Domain organization of [LCK_HUMAN] by SWISSPFAM
  • Domain found in 2ZYB: [TyrKc ] by SMART
  • Other resources with information on 2ZYB
  • Community annotation for 2ZYB 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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