1JY3 Blood Clotting date Sep 10, 2001
title Crystal Structure Of The Central Region Of Bovine Fibrinogen Fragment) At 1.4 Angstroms Resolution
authors J.Madrazo, J.H.Brown, S.Litvinovich, R.Dominguez, S.Yakovlev, L.M C.Cohen
compound source
Molecule: Fibrinogen Alpha Chain
Chain: N, Q
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Other_details: Proteolytic Fragment

Molecule: Fibrinogen Beta Chain
Chain: O, R

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Other_details: Proteolytic Fragment

Molecule: Fibrinogen Gamma-B Chain
Chain: P, S

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Other_details: Proteolytic Fragment
symmetry Space Group: P 21 21 21
R_factor 0.194 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.700 59.100 97.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
related structures by homologous chain: 1JY2
Gene
Ontology
ChainFunctionProcessComponent
O, R


Q, N


S, P


Primary referenceCrystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4-A resolution., Madrazo J, Brown JH, Litvinovich S, Dominguez R, Yakovlev S, Medved L, Cohen C, Proc Natl Acad Sci U S A 2001 Oct 9;98(21):11967-72. PMID:11593005
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (1jy3.pdb1.gz) 52 Kb
  • CSU: Contacts of Structural Units for 1JY3
  • Likely Quarternary Molecular Structure file(s) for 1JY3
  • Structure Factors (311 Kb)
  • Retrieve 1JY3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JY3 from S2C, [Save to disk]
  • Re-refined 1jy3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JY3 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 1JY3
  • 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
  • 3D motif for 1JY3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jy3n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1jy3o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1jy3p_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1jy3q_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1jy3r_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1jy3s_, region S [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1jy3_R] [1jy3_S] [1jy3] [1jy3_P] [1jy3_O] [1jy3_Q] [1jy3_N]
  • SWISS-PROT database: [P02672] [P02676] [P12799]
  • Domain organization of [FIBA_BOVIN] [FIBB_BOVIN] [FIBG_BOVIN] by SWISSPFAM
  • Other resources with information on 1JY3
  • Community annotation for 1JY3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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