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
  • Alignments of the sequence of 3PTA with the sequences similar proteins can be viewed for 3PTA's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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