2YYR Metal Binding Protein date May 01, 2007
title Structural Analysis Of Phd Domain Of Pygopus Complexed With Trimethylated Histone H3 Peptide
authors Y.Nakamura, B.Padmanabhan, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Pygopus Homolog 1
Chain: A, B
Fragment: Phd Domain
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Cell-Free Protein Synthesis
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcr2.1-Topo

Molecule: H3k4me3 Peptide
Chain: P
Engineered: Yes
Synthetic: Yes
Other_details: Synthesized Histone H3 Peptide, Tri- Methylated At Lys4
symmetry Space Group: P 43 21 2
R_factor 0.213 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.518 59.518 95.853 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand M3L, MSE, ZN enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (26 Kb) [Save to disk]
  • Biological Unit Coordinates (2yyr.pdb1.gz) 22 Kb
  • LPC: Ligand-Protein Contacts for 2YYR
  • CSU: Contacts of Structural Units for 2YYR
  • Likely Quarternary Molecular Structure file(s) for 2YYR
  • Retrieve 2YYR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YYR from S2C, [Save to disk]
    • View 2YYR 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 2YYR
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2YYR, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yyr_P] [2yyr_A] [2yyr_B] [2yyr]
  • SWISS-PROT database: [Q9D0P5]
  • Domain organization of [PYGO1_MOUSE] by SWISSPFAM
  • Domain found in 2YYR: [PHD ] by SMART
    • Other resources with information on 2YYR
  • Community annotation for 2YYR 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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