3TZD Transcription Dna Binding Protein date Sep 27, 2011
title Crystal Structure Of The Complex Of Human Chromobox Homolog
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 3
Chain: A
Fragment: Unp Residues 29-81
Synonym: Hech, Heterochromatin Protein 1 Homolog Gamma, Hp1 Modifier 2 Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cbx3

Molecule: Histone H1.4
Chain: T
Fragment: Unp Residues 19-36
Synonym: Histone H1b
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h1e, H1f4
symmetry Space Group: I 2 3
R_factor 0.199 R_Free 0.231
length a length b length c angle alpha angle beta angle gamma
92.209 92.209 92.209 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.81 Å
ligand MLY enzyme

Primary referenceStructural basis of the chromodomain of Cbx3 bound to methylated peptides from histone h1 and G9a., Ruan J, Ouyang H, Amaya MF, Ravichandran M, Loppnau P, Min J, Zang J, PLoS One. 2012;7(4):e35376. doi: 10.1371/journal.pone.0035376. Epub 2012 Apr 13. PMID:22514736
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (19 Kb) [Save to disk]
  • Biological Unit Coordinates (3tzd.pdb1.gz) 15 Kb
  • LPC: Ligand-Protein Contacts for 3TZD
  • CSU: Contacts of Structural Units for 3TZD
  • Structure Factors (180 Kb)
  • Retrieve 3TZD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3TZD from S2C, [Save to disk]
  • Re-refined 3tzd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3TZD 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 3TZD
  • 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 3TZD, from MSDmotif at EBI
  • Fold representative 3tzd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3tzd_T] [3tzd_A] [3tzd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3TZD: [CHROMO ] by SMART
  • Other resources with information on 3TZD
  • Community annotation for 3TZD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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