1YD9 Structural Protein date Dec 23, 2004
title 1.6a Crystal Structure Of The Non-Histone Domain Of The Hist Variant Macroh2a1.1.
authors S.Chakravarthy, G.Y.S.K.Swamy, C.Caron, P.Y.Perche, J.R.Pehrson, S.Khochbin, K.Luger
compound source
Molecule: Core Histone Macro-H2a.1
Chain: A, B, C, D
Fragment: Non-Histone Domain
Synonym: Histone Macroh2a1, Mh2a1, H2a.Y, H2ay
Engineered: Yes
 Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Gene: H2afy
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.235 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.114 89.791 95.679 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand AU enzyme
Primary referenceStructural characterization of the histone variant macroH2A., Chakravarthy S, Gundimella SK, Caron C, Perche PY, Pehrson JR, Khochbin S, Luger K, Mol Cell Biol 2005 Sep;25(17):7616-24. PMID:16107708
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (1yd9.pdb1.gz) 32 Kb
  • Biological Unit Coordinates (1yd9.pdb2.gz) 32 Kb
  • Biological Unit Coordinates (1yd9.pdb3.gz) 32 Kb
  • Biological Unit Coordinates (1yd9.pdb4.gz) 31 Kb
  • LPC: Ligand-Protein Contacts for 1YD9
  • CSU: Contacts of Structural Units for 1YD9
  • Likely Quarternary Molecular Structure file(s) for 1YD9
  • Structure Factors (1277 Kb)
  • Retrieve 1YD9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YD9 from S2C, [Save to disk]
  • Re-refined 1yd9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1YD9 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 1YD9
  • 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
  • 3D motif for 1YD9, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yd9_D] [1yd9_A] [1yd9] [1yd9_C] [1yd9_B]
  • SWISS-PROT database: [Q02874]
  • Domain organization of [H2AY_RAT] by SWISSPFAM
  • Domain found in 1YD9: [A1pp ] by SMART
    • Other resources with information on 1YD9
  • Community annotation for 1YD9 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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