3PDN Transferase Transferase Inhibitor date Oct 23, 2010
title Crystal Structure Of Smyd3 In Complex With Methyltransferase Sinefungin
authors N.Sirinupong, J.Brunzelle, Z.Yang
compound source
Molecule: Set And Mynd Domain-Containing Protein 3
Chain: A
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
symmetry Space Group: P 21 21 21
R_factor 0.155 R_Free 0.189
length a length b length c angle alpha angle beta angle gamma
61.240 66.246 107.384 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand GOL, MG, SFG, ZN enzyme Transferase E.C. BRENDA

Primary referenceStructural Insights into the Autoinhibition and Posttranslational Activation of Histone Methyltransferase SmyD3., Sirinupong N, Brunzelle J, Doko E, Yang Z, J Mol Biol. 2010 Dec 15. PMID:21167177
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (163 Kb) [Save to disk]
  • Biological Unit Coordinates (3pdn.pdb1.gz) 156 Kb
  • LPC: Ligand-Protein Contacts for 3PDN
  • CSU: Contacts of Structural Units for 3PDN
  • Structure Factors (359 Kb)
  • Retrieve 3PDN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PDN from S2C, [Save to disk]
  • Re-refined 3pdn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PDN 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 3PDN
  • 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 3PDN, from MSDmotif at EBI
  • Fold representative 3pdn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pdn_A] [3pdn]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PDN: [SET ] by SMART
  • Other resources with information on 3PDN
  • Community annotation for 3PDN 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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