3X04 Transferase date Oct 09, 2014
title Crystal Structure Of Pip4kiibeta Complex With Gmppnp
authors K.Takeuchi, Y.H.Lo, K.Sumita, M.Senda, J.Terakawa, A.Dimitoris, J.W.Locasale, M.Sasaki, H.Yoshino, Y.Zhang, E.R.Kahoud, T.Takano T.Yokota, B.Emerling, J.A.Asara, T.Ishida, I.Shimada, T.Daikoku, L.C.Cantley, T.Senda, A.T.Sasaki
compound source
Molecule: Phosphatidylinositol 5-Phosphate 4-Kinase Type-2
Chain: A, B
Fragment: Unp Residues 31-416
Synonym: 1-Phosphatidylinositol 5-Phosphate 4-Kinase 2-Beta Diphosphoinositide Kinase 2-Beta, Phosphatidylinositol 5-Ph Kinase Type II Beta, Pi(5)P 4-Kinase Type II Beta, Pip4kii- Ptdins(5)P-4-Kinase Isoform 2-Beta;
Ec: 2.7.1.149
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pip4k2b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.229 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
109.804 185.222 106.449 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand GNP enzyme Transferase E.C.2.7.1.149 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • phosphatidylinositol phospha...
  • 1-phosphatidylinositol-4-pho...
  • 1-phosphatidylinositol-5-pho...


  • Primary referenceThe Lipid Kinase PI5P4Kbeta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis., Sumita K, Lo YH, Takeuchi K, Senda M, Kofuji S, Ikeda Y, Terakawa J, Sasaki M, Yoshino H, Majd N, Zheng Y, Kahoud ER, Yokota T, Emerling BM, Asara JM, Ishida T, Locasale JW, Daikoku T, Anastasiou D, Senda T, Sasaki AT, Mol Cell. 2016 Jan 21;61(2):187-98. doi: 10.1016/j.molcel.2015.12.011. Epub 2016 , Jan 7. PMID:26774281
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (228 Kb) [Save to disk]
  • Biological Unit Coordinates (3x04.pdb1.gz) 220 Kb
  • LPC: Ligand-Protein Contacts for 3X04
  • CSU: Contacts of Structural Units for 3X04
  • Structure Factors (517 Kb)
  • Retrieve 3X04 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3X04 from S2C, [Save to disk]
  • Re-refined 3x04 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3X04 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 3X04
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 3x04 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3x04_A] [3x04_B] [3x04]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3X04: [PIPKc ] by SMART
  • Other resources with information on 3X04
  • Community annotation for 3X04 at PDBWiki (http://pdbwiki.org)

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