5JHN Transferase date Apr 21, 2016
title Structure Of G9a Set-Domain With Histone H3k9ala Mutant Pept Bound S-Adenosylmethionine
authors H.Jayaram, S.F.Bellon, F.Poy
compound source
Molecule: Histone-Lysine N-Methyltransferase Ehmt2
Chain: A, B
Fragment: Unp Residues 882-1155
Synonym: Euchromatic Histone-Lysine N-Methyltransferase 2,H Associated Transcript 8,Histone H3-K9 Methyltransferase 3,H Hmtase 3,Lysine N-Methyltransferase 1c,Protein G9a;
Ec: 2.1.1.-,
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ehmt2, Bat8, C6orf30, G9a, Kmt1c, Ng36
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) Rosetta

Molecule: Histone H3.1 Peptide With K9a Mutation
Chain: F, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.209 R_Free 0.237
length a length b length c angle alpha angle beta angle gamma
56.782 78.270 73.121 90.00 90.34 90.00
method X-Ray Diffractionresolution 1.67 Å
ligand SAM, ZN enzyme Transferase E.C.2.1.1 BRENDA
A, B

Primary referenceS-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3., Jayaram H, Hoelper D, Jain SU, Cantone N, Lundgren SM, Poy F, Allis CD, Cummings R, Bellon S, Lewis PW, Proc Natl Acad Sci U S A. 2016 May 31;113(22):6182-7. doi:, 10.1073/pnas.1605523113. Epub 2016 May 16. PMID:27185940
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk]
  • Biological Unit Coordinates (5jhn.pdb1.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 5JHN
  • CSU: Contacts of Structural Units for 5JHN
  • Structure Factors (1606 Kb)
  • Retrieve 5JHN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JHN from S2C, [Save to disk]
  • Re-refined 5jhn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5JHN 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 5JHN
  • 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 5jhn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jhn_B] [5jhn_G] [5jhn_F] [5jhn_A] [5jhn]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JHN: [PostSET] [PreSET] [SET ] by SMART
  • Other resources with information on 5JHN
  • Community annotation for 5JHN at PDBWiki (http://pdbwiki.org)

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