3ME3 Transferase date Mar 31, 2010
title Activator-Bound Structure Of Human Pyruvate Kinase M2
authors B.Hong, S.Dimov, W.Tempel, D.Auld, C.Thomas, M.Boxer, J.K.Jianq, A.Skoumbourdis, S.Min, N.Southall, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, J.Inglese, H.Park, Structural Consortium (Sgc)
compound source
Molecule: Pyruvate Kinase Isozymes M1m2
Chain: A, B, C, D
Synonym: Pyruvate Kinase Muscle Isozyme, Pyruvate Kinase 2 Cytosolic Thyroid Hormone-Binding Protein, Cthbp, Thyroid H Binding Protein 1, Thbp1, Opa-Interacting Protein 3, Oip-3, Tumor M2-Pk;
Ec: 2.7.1.40
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pkm2, Oip3, Pk2, Pk3, Pkm
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)-V2r
Expression_system_plasmid: Pet28a-Lic
symmetry Space Group: P 1 21 1
R_factor 0.219 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.882 152.564 93.036 90.00 103.17 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand 3SZ, FBP, SO4, UNX BindingDB enzyme Transferase E.C.2.7.1.40 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referencePyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis., Anastasiou D, Yu Y, Israelsen WJ, Jiang JK, Boxer MB, Hong BS, Tempel W, Dimov S, Shen M, Jha A, Yang H, Mattaini KR, Metallo CM, Fiske BP, Courtney KD, Malstrom S, Khan TM, Kung C, Skoumbourdis AP, Veith H, Southall N, Walsh MJ, Brimacombe KR, Leister W, Lunt SY, Johnson ZR, Yen KE, Kunii K, Davidson SM, Christofk HR, Austin CP, Inglese J, Harris MH, Asara JM, Stephanopoulos G, Salituro FG, Jin S, Dang L, Auld DS, Park HW, Cantley LC, Thomas CJ, Heiden MG, Nat Chem Biol. 2012 Aug 26. doi: 10.1038/nchembio.1060. PMID:22922757
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (321 Kb) [Save to disk]
  • Biological Unit Coordinates (3me3.pdb1.gz) 313 Kb
  • LPC: Ligand-Protein Contacts for 3ME3
  • CSU: Contacts of Structural Units for 3ME3
  • Structure Factors (2388 Kb)
  • Retrieve 3ME3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ME3 from S2C, [Save to disk]
  • Re-refined 3me3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ME3 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 3ME3
  • 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 3ME3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3me3_C] [3me3_A] [3me3] [3me3_B] [3me3_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3ME3
  • Community annotation for 3ME3 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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