3DM1 Transcription date Jun 30, 2008
title Crystal Structure Of The Complex Of Human Chromobox Homolog With 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 3
Chain: A, C, E, G
Fragment: Chromo 1 Domain: Residues 29-86
Synonym: Heterochromatin Protein 1 Homolog Gamma, Hp1 Gamma Protein, Hech;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Cbx3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Histone-Lysine N-Methyltransferase, H3 Lysine-9 S
Chain: B, D, F, H
Fragment: Unp Residues 179-190
Synonym: Histone H3-K9 Methyltransferase 3, H3-K9-Hmtase 3, Euchromatic Histone-Lysine N-Methyltransferase 2, Hla-B-Ass Transcript 8, Protein G9a, Lysine N-Methyltransferase 1c;
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide With The Sequence Matching Residues 179-190 Of The Human Histone H3-K9 Methyltransfera Ehmt2_human, Unp Entry Q96kq7
symmetry Space Group: P 32 2 1
R_factor 0.220 R_Free 0.267
length a length b length c angle alpha angle beta angle gamma
83.671 83.671 110.288 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand M3L enzyme
A, C, G, E

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] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (3dm1.pdb1.gz) 12 Kb
  • Biological Unit Coordinates (3dm1.pdb2.gz) 12 Kb
  • Biological Unit Coordinates (3dm1.pdb3.gz) 12 Kb
  • Biological Unit Coordinates (3dm1.pdb4.gz) 12 Kb
  • Biological Unit Coordinates (3dm1.pdb5.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 3DM1
  • CSU: Contacts of Structural Units for 3DM1
  • Likely Quarternary Molecular Structure file(s) for 3DM1
  • Structure Factors (127 Kb)
  • Retrieve 3DM1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DM1 from S2C, [Save to disk]
  • Re-refined 3dm1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DM1 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 3DM1
  • 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 3DM1, from MSDmotif at EBI
  • Fold representative 3dm1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dm1_G] [3dm1_C] [3dm1_D] [3dm1_E] [3dm1_A] [3dm1_H] [3dm1_F] [3dm1] [3dm1_B]
  • SWISS-PROT database: [Q13185] [Q96KQ7]
  • Domain organization of [CBX3_HUMAN] [EHMT2_HUMAN] by SWISSPFAM
  • Domain found in 3DM1: [CHROMO ] by SMART
  • Other resources with information on 3DM1
  • Community annotation for 3DM1 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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