3A1A Transferase date Mar 28, 2009
title Crystal Structure Of The Dnmt3a Add Domain
authors J.Otani, K.Arita, M.Ariyoshi, M.Shirakawa
compound source
Molecule: Dna (Cytosine-5)-Methyltransferase 3a
Chain: A
Fragment: Add(Atrx-Dnmt3-Dnmt3l) Domain, Residues 476-614
Synonym: Dnmt3a, Dna Methyltransferase Hsaiiia, Dna Mtase H M.Hsaiiia;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt3a
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p-1
symmetry Space Group: P 61 2 2
R_factor 0.209 R_Free 0.250
length a length b length c angle alpha angle beta angle gamma
57.581 57.581 138.949 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand EDO, ZN enzyme Transferase E.C. BRENDA

Primary referenceStructural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain., Otani J, Nankumo T, Arita K, Inamoto S, Ariyoshi M, Shirakawa M, EMBO Rep. 2009 Nov;10(11):1235-41. Epub 2009 Oct 16. PMID:19834512
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (31 Kb) [Save to disk]
  • Biological Unit Coordinates (3a1a.pdb1.gz) 22 Kb
  • LPC: Ligand-Protein Contacts for 3A1A
  • CSU: Contacts of Structural Units for 3A1A
  • Structure Factors (95 Kb)
  • Retrieve 3A1A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A1A from S2C, [Save to disk]
  • Re-refined 3a1a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A1A 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 3A1A
  • 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 3A1A, from MSDmotif at EBI
  • Fold representative 3a1a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a1a] [3a1a_A]
  • SWISS-PROT database: [Q9Y6K1]
  • Domain organization of [DNM3A_HUMAN] by SWISSPFAM
  • Other resources with information on 3A1A
  • Community annotation for 3A1A 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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