4WXX Transferase date Nov 14, 2014
title The Crystal Structure Of Human Dnmt1(351-1600)
authors Z.M.Zhang, J.Song
compound source
Molecule: Dna (Cytosine-5)-Methyltransferase 1
Chain: A, B
Synonym: Dnmt1, Cxxc-Type Zinc Finger Protein 9, Dna Methyltransferase 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
symmetry Space Group: P 43
R_factor 0.205 R_Free 0.245
length a length b length c angle alpha angle beta angle gamma
138.568 138.568 221.536 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.62 Å
ligand SAH, ZN enzyme Transferase E.C. BRENDA
A, B

Primary referenceCrystal Structure of Human DNA Methyltransferase 1., Zhang ZM, Liu S, Lin K, Luo Y, Perry JJ, Wang Y, Song J, J Mol Biol. 2015 Jun 10. pii: S0022-2836(15)00341-1. doi:, 10.1016/j.jmb.2015.06.001. PMID:26070743
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (395 Kb) [Save to disk]
  • Biological Unit Coordinates (4wxx.pdb1.gz) 197 Kb
  • Biological Unit Coordinates (4wxx.pdb2.gz) 198 Kb
  • LPC: Ligand-Protein Contacts for 4WXX
  • CSU: Contacts of Structural Units for 4WXX
  • Structure Factors (1902 Kb)
  • Retrieve 4WXX in mmCIF format [Save to disk]
  • Re-refined 4wxx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4WXX 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 4WXX
  • 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
  • Fold representative 4wxx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4wxx_A] [4wxx_B] [4wxx]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4WXX: [BAH ] by SMART
  • Other resources with information on 4WXX
  • Community annotation for 4WXX at PDBWiki (http://pdbwiki.org)

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