2OYI Blood Clotting date Feb 22, 2007
title Crystal Structure Of Fragment D Of Gammad298,301a Fibrinogen Peptide Ligand Gly-Pro-Arg-Pro-Amide
authors M.S.Kostelansky, O.V.Gorkun, S.T.Lord
compound source
Molecule: Fibrinogen Alpha Chain
Chain: A, D
Fragment: Residues 126-191
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fga
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_strain: Cho Cells

Molecule: Fibrinogen Beta Chain
Chain: B, E
Fragment: Residues 149-461
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fgb
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_strain: Cho Cells

Molecule: Fibrinogen Gamma Chain
Chain: C, F
Fragment: Residues 96-406
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fgg
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_strain: Cho Cells

Molecule: Gprp Peptide
Chain: G, H, I, J
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.988 94.038 226.353 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand CA, FUC, NAG enzyme
Primary referenceProbing the gamma2 Calcium-Binding Site: Studies with gammaD298,301A Fibrinogen Reveal Changes in the gamma294-301 Loop that Alter the Integrity of the "a" Polymerization Site(,)., Kostelansky MS, Lounes KC, Ping LF, Dickerson SK, Gorkun OV, Lord ST, Biochemistry. 2007 May 1;46(17):5114-23. Epub 2007 Apr 6. PMID:17411074
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (225 Kb) [Save to disk]
  • Biological Unit Coordinates (2oyi.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (2oyi.pdb2.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 2OYI
  • CSU: Contacts of Structural Units for 2OYI
  • Likely Quarternary Molecular Structure file(s) for 2OYI
  • Structure Factors (587 Kb)
  • Retrieve 2OYI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OYI from S2C, [Save to disk]
  • Re-refined 2oyi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OYI 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 2OYI
  • 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
  • 3D motif for 2OYI, from MSDmotif at EBI
  • Fold representative 2oyi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2oyi]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 2OYI: [FBG ] by SMART
  • Other resources with information on 2OYI
  • Community annotation for 2OYI 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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