3PT6 Transferase Dna date Dec 02, 2010
title Crystal Structure Of Mouse Dnmt1(650-1602) In Complex With D
authors J.Song, D.J.Patel
compound source
Molecule: Dna (Cytosine-5)-Methyltransferase 1
Chain: A, B
Fragment: Unp Residues 650-1602
Synonym: Dnmt1, Met-1, Dna Methyltransferase Mmui, Dna Mtas M.Mmui, Mcmt;
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Dnmt1, Dnmt, Met1, Uim
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21-Ril (De3)

Molecule: Dna (5'- D(Tpcpcpcpgptpgpapgpcpcptpcpcpgpcpapgpg)
Chain: C, D
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Cpcptpgpcpgpgpapgpgpcptpcpapcpgpgpgpa)
Chain: I, J
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.211 R_Free 0.266
length a length b length c angle alpha angle beta angle gamma
83.192 213.507 86.274 90.00 99.64 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand SAH, ZN BindingDB enzyme Transferase E.C. BRENDA
note 3PT6 (Molecule of the Month:pdb139)
A, B

Primary referenceStructure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation., Song J, Rechkoblit O, Bestor TH, Patel DJ, Science. 2010 Dec 16. PMID:21163962
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (322 Kb) [Save to disk]
  • Biological Unit Coordinates (3pt6.pdb1.gz) 160 Kb
  • Biological Unit Coordinates (3pt6.pdb2.gz) 159 Kb
  • LPC: Ligand-Protein Contacts for 3PT6
  • CSU: Contacts of Structural Units for 3PT6
  • Structure Factors (1555 Kb)
  • Retrieve 3PT6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PT6 from S2C, [Save to disk]
  • Re-refined 3pt6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PT6 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 3PT6
  • 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 3PT6, from MSDmotif at EBI
  • Fold representative 3pt6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pt6_J] [3pt6_D] [3pt6_A] [3pt6_I] [3pt6_B] [3pt6_C] [3pt6]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PT6: [BAH ] by SMART
  • Other resources with information on 3PT6
  • Community annotation for 3PT6 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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