5EMJ Transferase Transferase Inhibitor date Nov 06, 2015
title Crystal Structure Of Prmt5:Mep50 With Compound 8 And Sinefun
authors P.A.Boriack-Sjodin, L.Jin
compound source
Molecule: Protein Arginine N-Methyltransferase 5
Chain: A
Synonym: 72 Kda Icln-Binding Protein,Histone-Arginine N- Methyltransferase Prmt5,Jak-Binding Protein 1,Shk1 Kinase-B Protein 1 Homolog,Skb1hs;
Ec: 2.1.1.-,2.1.1.125
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prmt5, Hrmt1l5, Ibp72, Jbp1, Skb1
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Bacmid
Expression_system_plasmid: Pdest

Molecule: Methylosome Protein 50
Chain: B
Synonym: Mep-50,Androgen Receptor Cofactor P44,Wd Repeat-Co Protein 77,P44mep50;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Wdr77, Mep50, Wd45, Hkmt1069, Nbla10071
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Bacmid
Expression_system_plasmid: Pdest
symmetry Space Group: I 2 2 2
R_factor 0.209 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.240 138.830 179.340 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.27 Å
ligand 5QJ, GOL, SFG enzyme Transferase E.C.2.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • transcription corepressor ac...
  • protein-arginine omega-N sym...


  • B
  • ligand-dependent nuclear rec...


  • Primary referenceStructure and Property Guided Design in the Identification of PRMT5 Tool Compound EPZ015666., Duncan KW, Rioux N, Boriack-Sjodin PA, Munchhof MJ, Reiter LA, Majer CR, Jin L, Johnston LD, Chan-Penebre E, Kuplast KG, Porter Scott M, Pollock RM, Waters NJ, Smith JJ, Moyer MP, Copeland RA, Chesworth R, ACS Med Chem Lett. 2015 Dec 2;7(2):162-6. doi: 10.1021/acsmedchemlett.5b00380., eCollection 2016 Feb 11. PMID:26985292
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (166 Kb) [Save to disk]
  • Biological Unit Coordinates (5emj.pdb1.gz) 625 Kb
  • LPC: Ligand-Protein Contacts for 5EMJ
  • CSU: Contacts of Structural Units for 5EMJ
  • Structure Factors (1265 Kb)
  • Retrieve 5EMJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EMJ from S2C, [Save to disk]
  • Re-refined 5emj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EMJ 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 5EMJ
  • 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 5emj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5emj_A] [5emj_B] [5emj]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5EMJ: [WD40 ] by SMART
  • Other resources with information on 5EMJ
  • Community annotation for 5EMJ at PDBWiki (http://pdbwiki.org)

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