5GVD Protein Binding date Sep 05, 2016
title Human Tdrd3 Duf1767-Ob Domains
authors S.Goto-Ito, A.Yamagata, Y.Sato, T.S.Takahashi, S.Fukai
compound source
Molecule: Tudor Domain-Containing Protein 3
Chain: A, B
Fragment: Unp Residues 1-161
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tdrd3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 65
R_factor 0.175 R_Free 0.199
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.669 85.669 104.207 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.62 Å
ligand EDO, MG, PO4 enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (5gvd.pdb1.gz) 26 Kb
  • Biological Unit Coordinates (5gvd.pdb2.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 5GVD
  • CSU: Contacts of Structural Units for 5GVD
  • Structure Factors (1075 Kb)
  • Retrieve 5GVD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GVD from S2C, [Save to disk]
  • Re-refined 5gvd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5GVD 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 5GVD
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gvd_B] [5gvd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5GVD
  • Community annotation for 5GVD at PDBWiki (http://pdbwiki.org)

    • 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