1PFB Peptide Binding Protein date May 24, 2003
title Structural Basis For Specific Binding Of Polycomb Chromodoma Histone H3 Methylated At K27
authors J.R.Min, Y.Zhang, R.M.Xu
compound source
Molecule: Polycomb Protein
Chain: A
Fragment: Chromodomain
Engineered: Yes
Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: Pc Or Cg7618
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H3, Embryonic
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized. It I Naturally Found In Strongylocentrotus Purpuratus.
symmetry Space Group: I 21 21 21
R_factor 0.197 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
32.429 77.033 77.273 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.40 Å
ligand ACY, BME, CL, M3L enzyme
note 1PFB is a representative structure
related structures by homologous chain: 1PDQ
Primary referenceStructural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27., Min J, Zhang Y, Xu RM, Genes Dev 2003 Aug 1;17(15):1823-8. PMID:12897052
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (19 Kb) [Save to disk]
  • Biological Unit Coordinates (1pfb.pdb1.gz) 15 Kb
  • Biological Unit Coordinates (1pfb.pdb2.gz) 29 Kb
  • LPC: Ligand-Protein Contacts for 1PFB
  • CSU: Contacts of Structural Units for 1PFB
  • Likely Quarternary Molecular Structure file(s) for 1PFB
  • Structure Factors (259 Kb)
  • Retrieve 1PFB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PFB from S2C, [Save to disk]
  • Re-refined 1pfb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PFB 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 1PFB
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1PFB 1PFBA 1PFBB from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1PFB, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pfba_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1pfb_A] [1pfb] [1pfb_B]
  • SWISS-PROT database: [P26017]
  • Domain organization of [PC_DROME] by SWISSPFAM
  • Domain found in 1PFB: [CHROMO ] by SMART
  • Other resources with information on 1PFB
  • Community annotation for 1PFB 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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