3EPZ Transferase date Sep 30, 2008
title Structure Of The Replication Foci-Targeting Sequence Of Huma Cytosine Methyltransferase Dnmt1
authors J.R.Walker, G.V.Avvakumov, S.Xue, Y.Li, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Struct Genomics Consortium (Sgc)
compound source
Molecule: Dna (Cytosine-5)-Methyltransferase 1
Chain: A, B
Fragment: Replication Foci-Targeting Sequence
Synonym: Dnmt1, Mcmt, Dna Methyltransferase Hsai, Dna Mtase M.Hsai, Cxxc-Type Zinc Finger Protein 9;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aim, Cxx9, Cxxc9, Dnmt, Dnmt1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl
symmetry Space Group: P 1 21 1
R_factor 0.213 R_Free 0.264
length a length b length c angle alpha angle beta angle gamma
57.544 59.768 96.286 90.00 92.31 90.00
method X-Ray Diffractionresolution 2.31 Å
ligand BGC, GOL, MSE, NA, ZN enzyme Transferase E.C. BRENDA
note 3EPZ is a representative structure
Primary referenceThe replication focus targeting sequence (RFTS) domain is a DNA-competitive inhibitor of Dnmt1., Syeda F, Fagan RL, Wean M, Avvakumov GV, Walker JR, Xue S, Dhe-Paganon S, Brenner C, J Biol Chem. 2011 Apr 29;286(17):15344-51. Epub 2011 Mar 9. PMID:21389349
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk]
  • Biological Unit Coordinates (3epz.pdb1.gz) 76 Kb
  • Biological Unit Coordinates (3epz.pdb2.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 3EPZ
  • CSU: Contacts of Structural Units for 3EPZ
  • Likely Quarternary Molecular Structure file(s) for 3EPZ
  • Structure Factors (444 Kb)
  • Retrieve 3EPZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EPZ from S2C, [Save to disk]
  • Re-refined 3epz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EPZ 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 3EPZ
  • 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 3EPZ, from MSDmotif at EBI
  • Fold representative 3epz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3epz_B] [3epz] [3epz_A]
  • SWISS-PROT database: [P26358]
  • Domain organization of [DNMT1_HUMAN] by SWISSPFAM
  • Other resources with information on 3EPZ
  • Community annotation for 3EPZ 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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