5VVM Cell Adhesion date May 19, 2017
title Crystal Structure Of Human Cdh23 Ec21-23
authors A.Patel, A.Jaiganesh, M.Sotomayor
compound source
Molecule: Cadherin-23
Chain: A, B
Fragment: Residues 2169-2505
Synonym: Otocadherin
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdh23, Kiaa1774, Kiaa1812, Unq1894pro4340
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21-Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21-A+
symmetry Space Group: C 1 2 1
R_factor 0.303 R_Free 0.346
length a length b length c angle alpha angle beta angle gamma
116.714 166.806 47.930 90.00 102.53 90.00
method X-Ray Diffractionresolution 3.54 Å
ligand CA enzyme
A, B

Primary referenceZooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness., Jaiganesh A, De-la-Torre P, Patel AA, Termine DJ, Velez-Cortes F, Chen C, Sotomayor M, Structure. 2018 Jun 27. pii: S0969-2126(18)30209-0. doi:, 10.1016/j.str.2018.06.003. PMID:30033219
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (206 Kb) [Save to disk]
  • Biological Unit Coordinates (5vvm.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (5vvm.pdb2.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 5VVM
  • CSU: Contacts of Structural Units for 5VVM
  • Structure Factors (161 Kb)
  • Retrieve 5VVM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VVM from S2C, [Save to disk]
  • View 5VVM 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 5VVM
  • 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 5vvm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vvm_A] [5vvm_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VVM
  • Community annotation for 5VVM at PDBWiki (http://pdbwiki.org)

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