5HYN Transferase date Feb 01, 2016
title Structure Of Human Polycomb Repressive Complex 2 (Prc2) With Histone H3k27m Peptide
authors Y.Zhang, N.Justin, J.R.Wilson, S.J.Gamblin
compound source
Molecule: Histone-Lysine N-Methyltransferase Ezh2
Chain: A, F, K, Q
Synonym: Enx-1,Enhancer Of Zeste Homolog 2,Lysine N-Methylt 6;
Ec: 2.1.1.43
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ezh2, Kmt6
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Polycomb Protein Eed
Chain: B, G, L, R
Synonym: Heed,Wd Protein Associating With Integrin Cytoplas 1,Wait-1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Eed
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Polycomb Protein Suz12
Chain: C, H, M, S
Synonym: Chromatin Precipitated E2f Target 9 Protein,Chet 9 Joined To Jazf1 Protein,Suppressor Of Zeste 12 Protein Homo
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Suz12, Chet9, Jjaz1, Kiaa0160
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: H3k27m
Chain: D, I, O, T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Jarid2 K116me3
Chain: E, J, P, U
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.219 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
131.640 171.510 274.550 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.95 Å
ligand M3L, SAH, ZN enzyme Transferase E.C.2.1.1.43 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
B, R, G, L


F, A, K, Q


Primary referenceStructural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2., Justin N, Zhang Y, Tarricone C, Martin SR, Chen S, Underwood E, De Marco V, Haire LF, Walker PA, Reinberg D, Wilson JR, Gamblin SJ, Nat Commun. 2016 Apr 28;7:11316. doi: 10.1038/ncomms11316. PMID:27121947
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1455 Kb) [Save to disk]
  • Biological Unit Coordinates (5hyn.pdb1.gz) 372 Kb
  • Biological Unit Coordinates (5hyn.pdb2.gz) 369 Kb
  • Biological Unit Coordinates (5hyn.pdb3.gz) 366 Kb
  • Biological Unit Coordinates (5hyn.pdb4.gz) 367 Kb
  • Biological Unit Coordinates (5hyn.pdb5.gz) 370 Kb
  • Biological Unit Coordinates (5hyn.pdb6.gz) 367 Kb
  • Biological Unit Coordinates (5hyn.pdb7.gz) 364 Kb
  • Biological Unit Coordinates (5hyn.pdb8.gz) 365 Kb
  • LPC: Ligand-Protein Contacts for 5HYN
  • CSU: Contacts of Structural Units for 5HYN
  • Structure Factors (8839 Kb)
  • Retrieve 5HYN in mmCIF format [Save to disk]
  • Re-refined 5hyn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5HYN 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 5HYN
  • 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: [5hyn_R] [5hyn_B] [5hyn_Q] [5hyn_P] [5hyn_S] [5hyn_H] [5hyn_D] [5hyn_O] [5hyn_F] [5hyn_J] [5hyn_I] [5hyn_G] [5hyn_L] [5hyn] [5hyn_T] [5hyn_A] [5hyn_K] [5hyn_C] [5hyn_M] [5hyn_E] [5hyn_U]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5HYN: [CXC] [SANT] [SET] [WD40 ] by SMART
  • Other resources with information on 5HYN
  • Community annotation for 5HYN at PDBWiki (http://pdbwiki.org)

  • 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, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science