3PTA Transferase Dna date Dec 02, 2010
title Crystal Structure Of Human Dnmt1(646-1600) In Complex With D
authors J.Song, D.J.Patel
compound source
Molecule: Dna (Cytosine-5)-Methyltransferase 1
Chain: A
Fragment: Unp Residues 646-1600
Synonym: Dnmt1, Cxxc-Type Zinc Finger Protein 9, Dna Methyltransferase Hsai, Dna Mtase Hsai, M.Hsai, Mcmt;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt1, Aim, Cxxc9, Dnmt
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C41(De3)

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

Synthetic: Yes

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

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.257 R_Free 0.291
length a length b length c angle alpha angle beta angle gamma
162.800 87.900 113.900 90.00 97.20 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand SAH, ZN BindingDB enzyme Transferase E.C. BRENDA

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] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (3pta.pdb1.gz) 150 Kb
  • LPC: Ligand-Protein Contacts for 3PTA
  • CSU: Contacts of Structural Units for 3PTA
  • Structure Factors (121 Kb)
  • Retrieve 3PTA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PTA from S2C, [Save to disk]
  • Re-refined 3pta structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PTA 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 3PTA
  • 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 3PTA, from MSDmotif at EBI
  • Fold representative 3pta from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pta] [3pta_C] [3pta_A] [3pta_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PTA: [BAH ] by SMART
  • Other resources with information on 3PTA
  • Community annotation for 3PTA 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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