3FDR Rna Binding Protein date Nov 26, 2008
title Crystal Structure Of Tdrd2
authors M.F.Amaya, M.A.Adams, Y.Guo, Y.Li, I.Kozieradzki, A.M.Edwards, C.H.Arrowsmith, J.Weigelt, C.Bountra, A.Bochkarev, J.Min, Struct Genomics Consortium (Sgc)
compound source
Molecule: Tudor And Kh Domain-Containing Protein
Chain: A
Fragment: Tudor Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tdrkh, Tdrd2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15
symmetry Space Group: P 21 21 21
R_factor 0.214 R_Free 0.257
length a length b length c angle alpha angle beta angle gamma
41.565 45.106 46.561 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.75 Å
note 3FDR is a representative structure
Primary referenceMouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi., Chen C, Jin J, James DA, Adams-Cioaba MA, Park JG, Guo Y, Tenaglia E, Xu C, Gish G, Min J, Pawson T, Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20336-41. Epub 2009 Nov 16. PMID:19918066
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (20 Kb) [Save to disk]
  • Biological Unit Coordinates (3fdr.pdb1.gz) 16 Kb
  • CSU: Contacts of Structural Units for 3FDR
  • Likely Quarternary Molecular Structure file(s) for 3FDR
  • Structure Factors (57 Kb)
  • Retrieve 3FDR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FDR from S2C, [Save to disk]
  • Re-refined 3fdr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FDR 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 3FDR
  • 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 3FDR, from MSDmotif at EBI
  • Fold representative 3fdr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fdr_A] [3fdr]
  • SWISS-PROT database: [Q9Y2W6]
  • Domain organization of [TDRKH_HUMAN] by SWISSPFAM
  • Domain found in 3FDR: [TUDOR ] by SMART
  • Other resources with information on 3FDR
  • Community annotation for 3FDR 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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