3R93 Cell Cycle date Mar 24, 2011
title Crystal Structure Of The Chromo Domain Of M-Phase Phosphopro Bound To H3k9me3 Peptide
authors J.Li, Z.Li, J.Ruan, C.Xu, Y.Tong, P.W.Pan, W.Tempel, L.Crombet, J.Mi Structural Genomics Consortium (Sgc)
compound source
Molecule: M-Phase Phosphoprotein 8
Chain: A, B, C, D
Synonym: Two Hybrid-Associated Protein 3 With Ranbpm, Twa3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mphosph8, Mpp8
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-V2r-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl

Molecule: H3k9me3 Peptide
Chain: E, F, G, H
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.220 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.148 74.005 72.609 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.06 Å
ligand M3L, UNX enzyme
Primary referenceStructural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9., Li J, Li Z, Ruan J, Xu C, Tong Y, Pan PW, Tempel W, Crombet L, Min J, Zang J, PLoS One. 2011;6(10):e25104. Epub 2011 Oct 12. PMID:22022377
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (3r93.pdb1.gz) 25 Kb
  • Biological Unit Coordinates (3r93.pdb2.gz) 25 Kb
  • Biological Unit Coordinates (3r93.pdb3.gz) 24 Kb
  • Biological Unit Coordinates (3r93.pdb4.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 3R93
  • CSU: Contacts of Structural Units for 3R93
  • Structure Factors (352 Kb)
  • Retrieve 3R93 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3R93 from S2C, [Save to disk]
  • Re-refined 3r93 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3R93 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 3R93
  • 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 3R93, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3r93] [3r93_C] [3r93_H] [3r93_A] [3r93_D] [3r93_G] [3r93_B] [3r93_F] [3r93_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3R93: [CHROMO ] by SMART
  • Other resources with information on 3R93
  • Community annotation for 3R93 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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