5JK9 Cell Adhesion date Apr 26, 2016
title Crystal Structure Of Human Izumo1
authors U.Ohto, H.Ishida, T.Shimizu
compound source
Molecule: Izumo Sperm-Egg Fusion Protein 1
Chain: A, B, C, D, E, F
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
symmetry Space Group: P 1
R_factor 0.194 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.936 75.067 108.885 77.65 79.11 70.66
method X-Ray Diffractionresolution 2.10 Å
ligand NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (467 Kb) [Save to disk]
  • Biological Unit Coordinates (5jk9.pdb1.gz) 83 Kb
  • Biological Unit Coordinates (5jk9.pdb2.gz) 79 Kb
  • Biological Unit Coordinates (5jk9.pdb3.gz) 81 Kb
  • Biological Unit Coordinates (5jk9.pdb4.gz) 73 Kb
  • Biological Unit Coordinates (5jk9.pdb5.gz) 80 Kb
  • Biological Unit Coordinates (5jk9.pdb6.gz) 82 Kb
  • LPC: Ligand-Protein Contacts for 5JK9
  • CSU: Contacts of Structural Units for 5JK9
  • Structure Factors (6558 Kb)
  • Retrieve 5JK9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JK9 from S2C, [Save to disk]
  • Re-refined 5jk9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5JK9 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 5JK9
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jk9_C] [5jk9] [5jk9_F] [5jk9_E] [5jk9_D] [5jk9_A] [5jk9_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5JK9: [IG ] by SMART
    • Other resources with information on 5JK9
  • Community annotation for 5JK9 at PDBWiki (http://pdbwiki.org)

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