3RIB Transferase date Apr 13, 2011
title Human Lysine Methyltransferase Smyd2 In Complex With Adohcy
authors S.Xu, T.Zhang, C.Zhong, J.Ding
compound source
Molecule: N-Lysine Methyltransferase Smyd2
Chain: A, B
Synonym: Hskm-B, Histone Methyltransferase Smyd2, Lysine N- Methyltransferase 3c, Set And Mynd Domain-Containing Protei
Ec: 2.1.1.-,
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Smyd2, Kmt3c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: C 1 2 1
R_factor 0.246 R_Free 0.300
length a length b length c angle alpha angle beta angle gamma
194.560 57.185 96.607 90.00 103.95 90.00
method X-Ray Diffractionresolution 2.79 Å
ligand SAH, SO4, ZN enzyme Transferase E.C.2.1.1 BRENDA
A, B
  • histone methyltransferase ac...

  • Primary referenceStructure of human lysine methyltransferase Smyd2 reveals insights into the substrate divergence in Smyd proteins., Xu S, Zhong C, Zhang T, Ding J, J Mol Cell Biol. 2011 Jul 1. PMID:21724641
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (3rib.pdb1.gz) 72 Kb
  • Biological Unit Coordinates (3rib.pdb2.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 3RIB
  • CSU: Contacts of Structural Units for 3RIB
  • Structure Factors (332 Kb)
  • Retrieve 3RIB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RIB from S2C, [Save to disk]
  • Re-refined 3rib structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
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  • Visual 3D analysis of 3RIB
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  • 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
  • 3D motif for 3RIB, from MSDmotif at EBI
  • Fold representative 3rib from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rib_A] [3rib] [3rib_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3RIB: [SET ] by SMART
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  • Community annotation for 3RIB at PDBWiki (http://pdbwiki.org)
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