3F9W Transferase date Nov 14, 2008
title Structural Insights Into Lysine Multiple Methylation By Set 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 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 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
A, D, C, B

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] (265 Kb) [Save to disk]
  • Biological Unit Coordinates (3f9w.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (3f9w.pdb2.gz) 66 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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