3HNA Hydrolase Hydrolase Regulator date May 30, 2009
title Crystal Structure Of Catalytic Domain Of Human Euchromatic H Methyltransferase 1 In Complex With Sah And Mono-Methylated Peptide
authors J.Min, H.Wu, P.Loppnau, J.Wleigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, A.N.Plotnikov, Structural Genomics C (Sgc)
compound source
Molecule: Histone-Lysine N-Methyltransferase, H3 Lysine-9 S
Chain: A, B
Synonym: Histone H3-K9 Methyltransferase 5, H3-K9-Hmtase 5, Euchromatic Histone-Lysine N-Methyltransferase 1, Eu-Hmtase Like Protein 1, Glp1, Lysine N-Methyltransferase 1d;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Bl21(De3)
Gene: Ehmt1, Euhmtase1, Kiaa1876, Kmt1d
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Mono-Methylated H3k9 Peptide
Chain: P, Q
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.166 R_Free 0.193
length a length b length c angle alpha angle beta angle gamma
83.526 83.372 95.130 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand MLZ, SAH, ZN enzyme Transferase E.C. BRENDA
note 3HNA is a representative structure
A, B

Primary referenceStructural biology of human H3K9 methyltransferases., Wu H, Min J, Lunin VV, Antoshenko T, Dombrovski L, Zeng H, Allali-Hassani A, Campagna-Slater V, Vedadi M, Arrowsmith CH, Plotnikov AN, Schapira M, PLoS One. 2010 Jan 11;5(1):e8570. PMID:20084102
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (3hna.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (3hna.pdb2.gz) 55 Kb
  • Biological Unit Coordinates (3hna.pdb3.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 3HNA
  • CSU: Contacts of Structural Units for 3HNA
  • Likely Quarternary Molecular Structure file(s) for 3HNA
  • Structure Factors (1606 Kb)
  • Retrieve 3HNA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HNA from S2C, [Save to disk]
  • Re-refined 3hna structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HNA 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 3HNA
  • 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 3HNA, from MSDmotif at EBI
  • Fold representative 3hna from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hna_Q] [3hna_B] [3hna_P] [3hna] [3hna_A]
  • SWISS-PROT database: [Q9H9B1]
  • Domain organization of [EHMT1_HUMAN] by SWISSPFAM
  • Domains found in 3HNA: [PreSET] [SET ] by SMART
  • Other resources with information on 3HNA
  • Community annotation for 3HNA at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science