4YC4 Transferase date Feb 19, 2015
title Crystal Structure Of Phosphatidyl Inositol 4-Kinase II Alpha Complex With Nucleotide Analog
authors M.Klima, E.Boura
compound source
Molecule: Phosphatidylinositol 4-Kinase Type 2-Alpha,Lysozy Phosphatidylinositol 4-Kinase Type 2-Alpha;
Chain: A
Synonym: Phosphatidylinositol 4-Kinase Type II-Alpha, Phosphatidylinositol 4-Kinase Type II-Alpha;
Engineered: Yes
Organism_scientific: Homo Sapiens, Enterobacteria Phage T4
Organism_common: Human
Organism_taxid: 9606, 10665
Gene: Pi4k2a, T4tp126
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfd
symmetry Space Group: P 21 21 2
R_factor 0.214 R_Free 0.256
length a length b length c angle alpha angle beta angle gamma
79.414 103.770 78.109 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.58 Å
ligand ADP, M59 enzyme Transferase E.C. BRENDA

Primary referenceThe high-resolution crystal structure of phosphatidylinositol 4-kinase IIbeta and the crystal structure of phosphatidylinositol 4-kinase IIalpha containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design., Klima M, Baumlova A, Chalupska D, Hrebabecky H, Dejmek M, Nencka R, Boura E, Acta Crystallogr D Biol Crystallogr. 2015 Jul 1;71(Pt 7):1555-63. doi:, 10.1107/S1399004715009505. Epub 2015 Jun 30. PMID:26143926
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (4yc4.pdb1.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 4YC4
  • CSU: Contacts of Structural Units for 4YC4
  • Structure Factors (174 Kb)
  • Retrieve 4YC4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YC4 from S2C, [Save to disk]
  • Re-refined 4yc4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YC4 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 4YC4
  • 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
  • Fold representative 4yc4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yc4] [4yc4_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4YC4
  • Community annotation for 4YC4 at PDBWiki (http://pdbwiki.org)

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