2XB1 Transcription date Apr 01, 2010
title Crystal Structure Of The Human Pygo2 Phd Finger In Complex W B9l Hd1 Domain
authors T.C.Miller, T.J.Rutherford, C.M.Johnson, M.Fiedler, M.Bienz
compound source
Molecule: Pygopus Homolog 2, B-Cell Clllymphoma 9-Like Pro
Chain: A, C
Fragment: Phd Finger And Hd1 Domain, Residues 325-387,232-2
Synonym: Pygopus 2, B-Cell Lymphoma 9-Like Protein, Bcl9-Li Protein, Bcl9-2, B9l;
Engineered: Yes
Other_details: Artificial Linker Between Phd Finger And Hd1 (7aa Linker-Gsgsgsg)
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Codonplus-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petm41-Hphd2gsghd1
symmetry Space Group: P 21 21 21
R_factor 0.171 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.750 69.730 82.070 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand GOL, PEG, ZN enzyme
Primary referenceAllosteric Remodelling of the Histone H3 Binding Pocket in the Pygo2 PHD Finger Triggered by Its Binding to the B9L/BCL9 Co-Factor., Miller TC, Rutherford TJ, Johnson CM, Fiedler M, Bienz M, J Mol Biol. 2010 Jul 14. PMID:20637214
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (2xb1.pdb1.gz) 34 Kb
  • Biological Unit Coordinates (2xb1.pdb2.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 2XB1
  • CSU: Contacts of Structural Units for 2XB1
  • Structure Factors (238 Kb)
  • Retrieve 2XB1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XB1 from S2C, [Save to disk]
  • Re-refined 2xb1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2XB1 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 2XB1
  • 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 2XB1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q2xb1, region B:1-133,B:358-371 [Jmol] [rasmolscript] [script source]
        - Domain d1n2xb1, region B:115-215 [Jmol] [rasmolscript] [script source]
        - Domain d1w2xb1, region B:1482-1814 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xb1_C] [2xb1_A] [2xb1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2XB1: [PHD ] by SMART
    • Other resources with information on 2XB1
  • Community annotation for 2XB1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science