3SX0 Transferase date Jul 14, 2011
title Crystal Structure Of Dot1l In Complex With A Brominated Sah
authors W.Yu, W.Tempel, D.Smil, M.Schapira, Y.Li, M.Vedadi, K.T.Nguyen, A.K.Wernimont, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigel P.J.Brown, Structural Genomics Consortium (Sgc)
compound source
Molecule: Histone-Lysine N-Methyltransferase, H3 Lysine-79
Chain: A
Fragment: Sequence Database Residues 1-420
Synonym: Dot1-Like Protein, Histone H3-K79 Methyltransferas Hmtase, Lysine N-Methyltransferase 4;
Ec: 2.1.1.43
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dot1l, Kiaa1814, Kmt4
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21-V2r-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl
symmetry Space Group: P 65
R_factor 0.210 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
152.917 152.917 50.964 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.28 Å
ligand SO4, SX0, UNX BindingDB enzyme Transferase E.C.2.1.1.43 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceBromo-deaza-SAH: a potent and selective DOT1L inhibitor., Yu W, Smil D, Li F, Tempel W, Fedorov O, Nguyen KT, Bolshan Y, Al-Awar R, Knapp S, Arrowsmith CH, Vedadi M, Brown PJ, Schapira M, Bioorg Med Chem. 2013 Apr 1;21(7):1787-1794. doi: 10.1016/j.bmc.2013.01.049. Epub, 2013 Jan 30. PMID:23433670
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (3sx0.pdb1.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 3SX0
  • CSU: Contacts of Structural Units for 3SX0
  • Structure Factors (458 Kb)
  • Retrieve 3SX0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SX0 from S2C, [Save to disk]
  • Re-refined 3sx0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SX0 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 3SX0
  • 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 3SX0, from MSDmotif at EBI
  • Fold representative 3sx0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3sx0] [3sx0_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3SX0: [AT_hook ] by SMART
  • Other resources with information on 3SX0
  • Community annotation for 3SX0 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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