3F9W Transferase date Nov 14, 2008
title Structural Insights Into Lysine Multiple Methylation By Set Domain Methyltransferases, Set8-Y334f H4-Lys20 Adohcy
authors J-F.Couture, L.M.A.Dirk, J.S.Brunzelle, R.L.Houtz, R.C.Trievel
compound source
Molecule: Histone-Lysine N-Methyltransferase Setd8
Chain: A, B, C, D
Fragment: Set Domain: Unp Residues 232-393
Synonym: H4-K20-Hmtase Setd8, Set Domain-Containing Protein 8, Prset Domain-Containing Protein 07, Prset07, Pr-Set7, Lysine N-Methyltransferase 5a;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Setd8, Kmt5a, Prset7, Set07, Set8
Expression_system: Escherichia Coli
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_vector: Parallel
Expression_system_plasmid: Phis2

Molecule: Histone H4
Chain: E, F, G, H
Fragment: Unp Residues 16-25
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide Corresponding To Residues 16-25 Of Human Histone H4
symmetry Space Group: P 1
R_factor 0.162 R_Free 0.206
length a length b length c angle alpha angle beta angle gamma
44.000 45.600 94.200 89.20 87.10 90.80
method X-Ray Diffractionresolution 1.60 Å
ligand SAH enzyme Transferase E.C. BRENDA
Primary referenceStructural origins for the product specificity of SET domain protein methyltransferases., Couture JF, Dirk LM, Brunzelle JS, Houtz RL, Trievel RC, Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20659-64. Epub 2008 Dec 16. PMID:19088188
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (266 Kb) [Save to disk]
  • Biological Unit Coordinates (3f9w.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (3f9w.pdb2.gz) 67 Kb
  • Biological Unit Coordinates (3f9w.pdb3.gz) 68 Kb
  • Biological Unit Coordinates (3f9w.pdb4.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 3F9W
  • CSU: Contacts of Structural Units for 3F9W
  • Likely Quarternary Molecular Structure file(s) for 3F9W
  • Structure Factors (1362 Kb)
  • Retrieve 3F9W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F9W from S2C, [Save to disk]
  • Re-refined 3f9w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F9W 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 3F9W
  • 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 3F9W, from MSDmotif at EBI
  • Fold representative 3f9w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f9w_A] [3f9w_F] [3f9w_D] [3f9w_G] [3f9w_H] [3f9w_C] [3f9w_E] [3f9w_B] [3f9w]
  • SWISS-PROT database: [P62805] [Q9NQR1]
  • Domain organization of [H4_HUMAN] [SETD8_HUMAN] by SWISSPFAM
  • Domain found in 3F9W: [SET ] by SMART
  • Other resources with information on 3F9W
  • Community annotation for 3F9W 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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