3LLR Transferase date Jan 29, 2010
title Crystal Structure Of The Pwwp Domain Of Human Dna (Cytosine- Methyltransferase 3 Alpha
authors W.Qiu, L.Dombrovski, S.Ni, J.Weigelt, C.Boutra, C.H.Arrowsmith, A.M.Edwards, J.Min, H.Wu, Structural Genomics Consortium (Sgc)
compound source
Molecule: Dna (Cytosine-5)-Methyltransferase 3a
Chain: A, B, C, D, E
Fragment: Pwwp Domain (Unp Residues 275-427)
Synonym: Dnmt3a, Dna Methyltransferase Hsaiiia, Dna Mtase H M.Hsaiiia;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt3a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.216 R_Free 0.256
length a length b length c angle alpha angle beta angle gamma
67.110 83.990 74.590 90.00 90.48 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand BTB, SO4 enzyme Transferase E.C. BRENDA
note 3LLR is a representative structure
A, D, C, E, B

Primary referenceStructural and Histone Binding Ability Characterizations of Human PWWP Domains., Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J, PLoS One. 2011;6(6):e18919. Epub 2011 Jun 20. PMID:21720545
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (121 Kb) [Save to disk]
  • Biological Unit Coordinates (3llr.pdb1.gz) 25 Kb
  • Biological Unit Coordinates (3llr.pdb2.gz) 25 Kb
  • Biological Unit Coordinates (3llr.pdb3.gz) 25 Kb
  • Biological Unit Coordinates (3llr.pdb4.gz) 27 Kb
  • Biological Unit Coordinates (3llr.pdb5.gz) 25 Kb
  • LPC: Ligand-Protein Contacts for 3LLR
  • CSU: Contacts of Structural Units for 3LLR
  • Structure Factors (553 Kb)
  • Retrieve 3LLR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LLR from S2C, [Save to disk]
  • Re-refined 3llr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LLR 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 3LLR
  • 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 3LLR, from MSDmotif at EBI
  • Fold representative 3llr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3llr_E] [3llr_A] [3llr_C] [3llr] [3llr_B] [3llr_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LLR: [PWWP ] by SMART
  • Other resources with information on 3LLR
  • Community annotation for 3LLR 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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