3QO4 Apoptosis date Feb 09, 2011
title The Crystal Structure Of Death Receptor 6
authors M.Kuester, S.Kemmerzehl, S.O.Dahms, D.Roeser, M.E.Than
compound source
Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: A
Fragment: Unp Residues 42-218
Synonym: Death Receptor 6
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfrsf21, Dr6, Unq437pro868
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origami2(De3)
symmetry Space Group: P 61 2 2
R_factor 0.215 R_Free 0.261
length a length b length c angle alpha angle beta angle gamma
77.910 77.910 187.844 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand ACT, SO4 enzyme
note 3QO4 is a representative structure
Primary referenceThe Crystal Structure of Death Receptor 6 (DR6): A Potential Receptor of the Amyloid Precursor Protein (APP)., Kuester M, Kemmerzehl S, Dahms SO, Roeser D, Than ME, J Mol Biol. 2011 Jun 3;409(2):189-201. Epub 2011 Apr 2. PMID:21463639
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (3qo4.pdb1.gz) 30 Kb
  • Biological Unit Coordinates (3qo4.pdb2.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 3QO4
  • CSU: Contacts of Structural Units for 3QO4
  • Structure Factors (153 Kb)
  • Retrieve 3QO4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QO4 from S2C, [Save to disk]
  • Re-refined 3qo4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QO4 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 3QO4
  • 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 3QO4, from MSDmotif at EBI
  • Fold representative 3qo4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qo4] [3qo4_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3QO4: [Ephrin_rec_like] [TNFR ] by SMART
  • Other resources with information on 3QO4
  • Community annotation for 3QO4 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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