5EQX Cell Adhesion date Nov 13, 2015
title Crystal Structure Of Human Desmoglein-3 Ectodomain
authors O.J.Harrison, J.Brasch, L.Shapiro
compound source
Molecule: Desmoglein-3
Chain: A
Synonym: 130 Kda Pemphigus Vulgaris Antigen,Pva,Cadherin Fa Member 6;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dsg3, Cdhf6
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
symmetry Space Group: P 1 2 1
R_factor 0.236 R_Free 0.273
length a length b length c angle alpha angle beta angle gamma
81.909 44.862 106.699 90.00 102.92 90.00
method X-Ray Diffractionresolution 3.05 Å
ligand CA, MAN, NAG enzyme

Primary referenceStructural basis of adhesive binding by desmocollins and desmogleins., Harrison OJ, Brasch J, Lasso G, Katsamba PS, Ahlsen G, Honig B, Shapiro L, Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):7160-5. doi:, 10.1073/pnas.1606272113. Epub 2016 Jun 13. PMID:27298358
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (146 Kb) [Save to disk]
  • Biological Unit Coordinates (5eqx.pdb1.gz) 139 Kb
  • LPC: Ligand-Protein Contacts for 5EQX
  • CSU: Contacts of Structural Units for 5EQX
  • Structure Factors (187 Kb)
  • Retrieve 5EQX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EQX from S2C, [Save to disk]
  • Re-refined 5eqx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EQX 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 5EQX
  • 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 5eqx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5eqx] [5eqx_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5EQX: [CA ] by SMART
  • Other resources with information on 5EQX
  • Community annotation for 5EQX at PDBWiki (http://pdbwiki.org)

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