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
crystal cell	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 Diffraction	resolution	2.40 Å
ligand	M3L	enzyme
Gene Ontology	Chain Function Process Component A, C, G, E
Primary reference	Structural 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

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 3DM1, from MSDmotif at EBI

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)

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