5J39 Transcription date Mar 30, 2016
title Crystal Structure Of The Extended Tudor Domain From Tdrd2
authors H.Zhang, W.Tempel, A.Dong, C.Bountra, C.H.Arrowsmith, A.M.Edwards Structural Genomics Consortium (Sgc)
compound source
Molecule: Tudor And Kh Domain-Containing Protein
Chain: A, B
Fragment: Unp Residues 309-498
Synonym: Tudor Domain-Containing Protein 2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tdrkh, Tdrd2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-V2r-Prare3
Expression_system_plasmid: Pet28mhl
symmetry Space Group: P 1 21 1
R_factor 0.190 R_Free 0.222
length a length b length c angle alpha angle beta angle gamma
36.692 53.798 108.063 90.00 84.26 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand CAC, UNX enzyme
Primary referenceStructural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2., Zhang H, Liu K, Izumi N, Huang H, Ding D, Ni Z, Sidhu SS, Chen C, Tomari Y, Min J, Proc Natl Acad Sci U S A. 2017 Nov 8. pii: 201711486. doi:, 10.1073/pnas.1711486114. PMID:29118143
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (136 Kb) [Save to disk]
  • Biological Unit Coordinates (5j39.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (5j39.pdb2.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 5J39
  • CSU: Contacts of Structural Units for 5J39
  • Structure Factors (3396 Kb)
  • Retrieve 5J39 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5J39 from S2C, [Save to disk]
  • Re-refined 5j39 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5J39 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 5J39
  • 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
  • Fold representative 5j39 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5j39] [5j39_A] [5j39_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5J39: [TUDOR ] by SMART
  • Other resources with information on 5J39
  • Community annotation for 5J39 at PDBWiki (http://pdbwiki.org)

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