5JKD Cell Adhesion date Apr 26, 2016
title Crystal Structure Of Human Izumo1-Juno Complex (Crystal Form
authors U.Ohto, H.Ishida, T.Shimizu
compound source
Molecule: Izumo Sperm-Egg Fusion Protein 1
Chain: A
Fragment: Unp Residues 22-255
Synonym: Oocyte Bindingfusion Factor,Obf,Sperm-Specific Pr Izumo;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Izumo1
Expression_system: Drosophila
Expression_system_taxid: 7215

Molecule: Sperm-Egg Fusion Protein Juno
Chain: B
Fragment: Unp Residues 20-228
Synonym: Folate Receptor 4,Folate Receptor Delta,Fr-Delta,I Receptor Protein Juno;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Izumo1r, Folr4, Juno
Expression_system: Drosophila
Expression_system_taxid: 7215
symmetry Space Group: C 1 2 1
R_factor 0.220 R_Free 0.251
length a length b length c angle alpha angle beta angle gamma
145.604 65.377 77.199 90.00 104.24 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand CL, NAG enzyme


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (152 Kb) [Save to disk]
  • Biological Unit Coordinates (5jkd.pdb1.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 5JKD
  • CSU: Contacts of Structural Units for 5JKD
  • Structure Factors (334 Kb)
  • Retrieve 5JKD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JKD from S2C, [Save to disk]
  • Re-refined 5jkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5JKD 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 5JKD
  • 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 5jkd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jkd_B] [5jkd] [5jkd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5JKD: [IG ] by SMART
  • Other resources with information on 5JKD
  • Community annotation for 5JKD at PDBWiki (http://pdbwiki.org)

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