5ERP Cell Adhesion date Nov 14, 2015
title Crystal Structure Of Human Desmocollin-2 Ectodomain Fragment
authors O.J.Harrison, J.Brasch, L.Shapiro
compound source
Molecule: Desmocollin-2
Chain: A, B
Fragment: Unp Residues 236-680
Synonym: Cadherin Family Member 2,Desmocollin-3,Desmosomal Glycoprotein II,Desmosomal Glycoprotein III;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dsc2, Cdhf2, Dsc3
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
symmetry Space Group: C 1 2 1
R_factor 0.224 R_Free 0.262
length a length b length c angle alpha angle beta angle gamma
146.216 94.166 126.307 90.00 93.66 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand BMA, CA, EDO, MAN, NAG, SO4 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] (291 Kb) [Save to disk]
  • Biological Unit Coordinates (5erp.pdb1.gz) 278 Kb
  • LPC: Ligand-Protein Contacts for 5ERP
  • CSU: Contacts of Structural Units for 5ERP
  • Structure Factors (1430 Kb)
  • Retrieve 5ERP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ERP from S2C, [Save to disk]
  • Re-refined 5erp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5ERP 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 5ERP
  • 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 5erp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5erp_B] [5erp] [5erp_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5ERP: [CA ] by SMART
  • Other resources with information on 5ERP
  • Community annotation for 5ERP at PDBWiki (http://pdbwiki.org)

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