2OYH	Blood Clotting	date	Feb 22, 2007
title	Crystal Structure Of Fragment D Of Gammad298,301a Fibrinogen Peptide Ligand Gly-His-Arg-Pro-Amide
authors	M.S.Kostelansky, O.V.Gorkun, S.T.Lord
compound		source
Molecule: Fibrinogen Alpha Chain Chain: A, D Fragment: Residues 145-210 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 179-491 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 122-432 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: Ghrp Peptide Chain: G, H, I, J Engineered: Yes		Synthetic: Yes Other_details: Ghrp Peptide Chemically Synthesized
symmetry	Space Group: P 21 21 21	R_factor 0.220 R_Free 0.259
crystal cell	length a length b length c angle alpha angle beta angle gamma 89.164 94.119 226.730 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	CA, FUC, NAG	enzyme
Gene Ontology	Chain Function Process Component E, B eukaryotic cell surface bind... chaperone binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle F, C eukaryotic cell surface bind... metal ion binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle
Primary reference	Probing 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] (228 Kb) [Save to disk] Biological Unit Coordinates (2oyh.pdb1.gz) 114 Kb Biological Unit Coordinates (2oyh.pdb2.gz) 111 Kb LPC: Ligand-Protein Contacts for 2OYH CSU: Contacts of Structural Units for 2OYH Likely Quarternary Molecular Structure file(s) for 2OYH Structure Factors (737 Kb) Retrieve 2OYH in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2OYH from S2C, [Save to disk] Re-refined 2oyh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2OYH 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2OYH

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 2OYH, from MSDmotif at EBI Fold representative 2oyh from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 2OYH: [FBG ] by SMART Alignments of the sequence of 2OYH with the sequences similar proteins can be viewed for 2OYH's classification [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2OYH

Community annotation for 2OYH at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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