3OXF Transferase date Sep 21, 2010
title Human Lysine Methyltransferase Smyd3 In Complex With Adohcy
authors S.Xu, J.Wu, B.Sun, C.Zhong, J.Ding
compound source
Molecule: Set And Mynd Domain-Containing Protein 3
Chain: A, B
Synonym: Zinc Finger Mynd Domain-Containing Protein 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Smyd3, Zmynd1, Znfn3a1
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: P 1 21 1
R_factor 0.211 R_Free 0.261
length a length b length c angle alpha angle beta angle gamma
57.991 117.990 82.808 90.00 91.78 90.00
method X-Ray Diffractionresolution 2.82 Å
ligand SAH, ZN enzyme Transferase E.C. BRENDA
A, B

Primary referenceStructural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding., Xu S, Wu J, Sun B, Zhong C, Ding J, Nucleic Acids Res. 2011 Jan 25. PMID:21266482
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (3oxf.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (3oxf.pdb2.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 3OXF
  • CSU: Contacts of Structural Units for 3OXF
  • Structure Factors (331 Kb)
  • Retrieve 3OXF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OXF from S2C, [Save to disk]
  • Re-refined 3oxf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OXF 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 3OXF
  • 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
  • 3D motif for 3OXF, from MSDmotif at EBI
  • Fold representative 3oxf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3oxf_B] [3oxf_A] [3oxf]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3OXF: [SET ] by SMART
  • Other resources with information on 3OXF
  • Community annotation for 3OXF 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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