3I90	Transcription	date	Jul 10, 2009
title	Crystal Structure Of Human Chromobox Homolog 6 (Cbx6) With H 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 6 Chain: A, B Fragment: Chromo Domain: Unp Residues 9-64 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Cbx6 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21-V2r-Prare2 Expression_system_vector_type: Plasmid
Molecule: H3k27 Peptide Chain: C, D Engineered: Yes		Synthetic: Yes Other_details: Synthetic Peptide
symmetry	Space Group: P 65 2 2	R_factor 0.252 R_Free 0.300
crystal cell	length a length b length c angle alpha angle beta angle gamma 53.421 53.421 227.778 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	M3L	enzyme
Primary reference	Recognition 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] (28 Kb) [Save to disk] Biological Unit Coordinates (3i90.pdb1.gz) 12 Kb Biological Unit Coordinates (3i90.pdb2.gz) 11 Kb LPC: Ligand-Protein Contacts for 3I90 CSU: Contacts of Structural Units for 3I90 Structure Factors (95 Kb) Retrieve 3I90 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3I90 from S2C, [Save to disk] Re-refined 3i90 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3I90 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3I90

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 3I90, from MSDmotif at EBI Fold representative 3i90 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3i90_A] [3i90_B] [3i90_C] [3i90_D] SWISS-PROT database: [O95503] Domain organization of [CBX6_HUMAN] by SWISSPFAM Domain found in 3I90: [CHROMO ] by SMART Alignments of the sequence of 3I90 with the sequences similar proteins can be viewed for 3I90's classification [CBX6_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [CBX6_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3I90

Community annotation for 3I90 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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