6W8D Transferase Dna date Mar 20, 2020
title Structure Of Dnmt3a (R882h) In Complex With Cgt Dna
authors H.Anteneh, 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
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt3a
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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
Expression_system_taxid: 562

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: H 3
R_factor 0.199 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
205.560 205.560 89.505 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand PYO, SAH enzyme Transferase E.C.2.1.1.37 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


C, B


Primary referenceStructural basis for impairment of DNA methylation by the DNMT3A R882H mutation., Anteneh H, Fang J, Song J, Nat Commun. 2020 May 8;11(1):2294. doi: 10.1038/s41467-020-16213-9. PMID:32385248
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (371 Kb) [Save to disk]
  • Biological Unit Coordinates (6w8d.pdb1.gz) 360 Kb
  • LPC: Ligand-Protein Contacts for 6W8D
  • CSU: Contacts of Structural Units for 6W8D
  • Structure Factors (1199 Kb)
  • Retrieve 6W8D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6W8D from S2C, [Save to disk]
  • View 6W8D 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 6W8D
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6w8d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6w8d_E] [6w8d_B] [6w8d_C] [6w8d_D] [6w8d_A] [6w8d_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6W8D
  • Community annotation for 6W8D at PDBWiki (http://pdbwiki.org)

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