3PMT Transcription date Nov 18, 2010
title Crystal Structure Of The Tudor Domain Of Human Tudor Domain- Protein 3
authors R.Lam, C.B.Bian, Y.H.Guo, C.Xu, J.Kania, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, J.Min, Structural Gen Consortium (Sgc)
compound source
Molecule: Tudor Domain-Containing Protein 3
Chain: A
Fragment: Tudor Domain, Unp Residues 553-611
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tdrd3
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21-(De3)-V2r-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl
symmetry Space Group: P 65
R_factor 0.178 R_Free 0.209
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.682 41.682 59.947 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.80 Å
ligand PG4 enzyme
note 3PMT is a representative structure
Primary referenceCrystal Structure of TDRD3 and Methyl-Arginine Binding Characterization of TDRD3, SMN and SPF30., Liu K, Guo Y, Liu H, Bian C, Lam R, Liu Y, Mackenzie F, Rojas LA, Reinberg D, Bedford MT, Xu RM, Min J, PLoS One. 2012;7(2):e30375. Epub 2012 Feb 17. PMID:22363433
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (24 Kb) [Save to disk]
  • Biological Unit Coordinates (3pmt.pdb1.gz) 19 Kb
  • LPC: Ligand-Protein Contacts for 3PMT
  • CSU: Contacts of Structural Units for 3PMT
  • Structure Factors (159 Kb)
  • Retrieve 3PMT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PMT from S2C, [Save to disk]
  • Re-refined 3pmt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PMT 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 3PMT
  • 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 3PMT, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pmt_A] [3pmt]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PMT: [TUDOR ] by SMART
  • Other resources with information on 3PMT
  • Community annotation for 3PMT 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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