5V22 Transferase date Mar 02, 2017
title Crystal Structure Of Human Setd2 Set-Domain In Complex With Peptide And Sah
authors Y.Zhang, L.Tong
compound source
Molecule: Histone-Lysine N-Methyltransferase Setd2
Chain: A
Fragment: Set Domain (Unp Residues 1435-1711)
Synonym: Hif-1,Huntingtin Yeast Partner B,Huntingtin-Intera Protein 1,Hip-1,Huntingtin-Interacting Protein B,Lysine N- Methyltransferase 3a,Set Domain-Containing Protein 2,Hset2,
Ec: 2.1.1.43
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Setd2, Hif1, Hypb, Kiaa1732, Kmt3a, Set2, Hspc069
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H3k36m Peptide
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.287 77.196 76.527 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand SAH, ZN enzyme Transferase E.C.2.1.1.43 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMolecular basis for the role of oncogenic histone mutations in modulating H3K36 methylation., Zhang Y, Shan CM, Wang J, Bao K, Tong L, Jia S, Sci Rep. 2017 Mar 3;7:43906. doi: 10.1038/srep43906. PMID:28256625
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (5v22.pdb1.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 5V22
  • CSU: Contacts of Structural Units for 5V22
  • Structure Factors (157 Kb)
  • Retrieve 5V22 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V22 from S2C, [Save to disk]
  • Re-refined 5v22 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5V22 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 5V22
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v22_A] [5v22] [5v22_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5V22
  • Community annotation for 5V22 at PDBWiki (http://pdbwiki.org)

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