6BRR Transferase Dna date Nov 30, 2017
title Crystal Structure Of Dnmt3a (R836a)-Dnmt3l In Complex With D Containing Two Cpg Sites
authors Z.M.Zhang, J.Song
compound source
Molecule: Dna (Cytosine-5)-Methyltransferase 3a
Chain: A, D
Synonym: Dnmt3a,Dna Methyltransferase Hsaiiia,M.Hsaiiia
Ec: 2.1.1.37
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt3a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna (Cytosine-5)-Methyltransferase 3-Like
Chain: B, C
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt3l
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna (25-Mer)
Chain: E, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: H 3
R_factor 0.199 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
205.005 205.005 89.358 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.97 Å
ligand
enzyme Transferase E.C.2.1.1.37 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


C, B


Primary referenceStructural basis for DNMT3A-mediated de novo DNA methylation., Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S, Ji D, Rothbart SB, Wang Y, Wang GG, Song J, Nature. 2018 Feb 15;554(7692):387-391. doi: 10.1038/nature25477. Epub 2018 Feb 7. PMID:29414941
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (368 Kb) [Save to disk]
  • Biological Unit Coordinates (6brr.pdb1.gz) 356 Kb
  • CSU: Contacts of Structural Units for 6BRR
  • Structure Factors (596 Kb)
  • Retrieve 6BRR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6BRR from S2C, [Save to disk]
  • View 6BRR 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 6BRR
  • 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
  • Fold representative 6brr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6brr_C] [6brr_E] [6brr_B] [6brr_D] [6brr_A] [6brr_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6BRR
  • Community annotation for 6BRR at PDBWiki (http://pdbwiki.org)

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