5IRY Cell Adhesion date Mar 15, 2016
title Crystal Structure Of Human Desmocollin-1 Ectodomain
authors J.Brasch, O.J.Harrison, L.Shapiro
compound source
Molecule: Desmocollin-1
Chain: A, B
Fragment: Unp Residues 135-676
Synonym: Cadherin Family Member 1,Desmosomal Glycoprotein 2 Dg2dg3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dsc1, Cdhf1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
symmetry Space Group: C 1 2 1
R_factor 0.249 R_Free 0.302
length a length b length c angle alpha angle beta angle gamma
213.806 66.174 141.633 90.00 127.15 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand BMA, CA, EDO, MAN, NAG enzyme
A, B

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] (345 Kb) [Save to disk]
  • Biological Unit Coordinates (5iry.pdb1.gz) 335 Kb
  • LPC: Ligand-Protein Contacts for 5IRY
  • CSU: Contacts of Structural Units for 5IRY
  • Structure Factors (371 Kb)
  • Retrieve 5IRY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IRY from S2C, [Save to disk]
  • Re-refined 5iry structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IRY 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 5IRY
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5iry from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5iry_B] [5iry] [5iry_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5IRY: [CA ] by SMART
  • Other resources with information on 5IRY
  • Community annotation for 5IRY at PDBWiki (http://pdbwiki.org)

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