3FDT Protein Binding date Nov 26, 2008
title Crystal Structure Of The Complex Of Human Chromobox Homolog With H3k9(Me)3 Peptide
authors M.F.Amaya, M.Ravichandran, P.Loppnau, I.Kozieradzki, A.M.Edwards C.H.Arrowsmith, J.Weigelt, C.Bountra, A.Bochkarev, J.Min, H.Ouya Structural Genomics Consortium (Sgc)
compound source
Molecule: Chromobox Protein Homolog 5
Chain: A
Synonym: Heterochromatin Protein 1 Homolog Alpha, Hp1 Alpha P25;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cbx5, Hp1a
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: H3k9(Me)3 Peptide
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.197 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.123 73.123 28.413 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand M3L enzyme
Primary referenceRecognition and specificity determinants of the human cbx chromodomains., Kaustov L, Ouyang H, Amaya M, Lemak A, Nady N, Duan S, Wasney GA, Li Z, Vedadi M, Schapira M, Min J, Arrowsmith CH, J Biol Chem. 2011 Jan 7;286(1):521-9. Epub 2010 Nov 3. PMID:21047797
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (16 Kb) [Save to disk]
  • Biological Unit Coordinates (3fdt.pdb1.gz) 11 Kb
  • LPC: Ligand-Protein Contacts for 3FDT
  • CSU: Contacts of Structural Units for 3FDT
  • Likely Quarternary Molecular Structure file(s) for 3FDT
  • Structure Factors (38 Kb)
  • Retrieve 3FDT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FDT from S2C, [Save to disk]
  • Re-refined 3fdt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3FDT 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 3FDT
  • 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 3FDT, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fdt_T] [3fdt_A] [3fdt]
  • SWISS-PROT database: [P45973]
  • Domain organization of [CBX5_HUMAN] by SWISSPFAM
  • Domain found in 3FDT: [CHROMO ] by SMART
    • Other resources with information on 3FDT
  • Community annotation for 3FDT 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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