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
  • Alignments of the sequence of 3PDN with the sequences similar proteins can be viewed for 3PDN's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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