2VR3	Cell Adhesion	date	Mar 25, 2008
title	Structural And Biochemical Characterization Of Fibrinogen Binding To Clfa From Staphylocccus Aureus
authors	V.K.Ganesh, J.J.Rivera, E.Smeds, M.G.Bowden, E.R.Wann, S.Gurusidappa, J.R.Fitzgerald, M.Hook
compound		source
Molecule: Clumping Factor A Chain: A, B Fragment: N2n3, Residues 229-545 Synonym: Fibrinogen-Binding Protein A, Fibrinogen Receptor A; Engineered: Yes Mutation: Yes Other_details: Engineered Disulfide Bond Between 327 And 541;		Organism_scientific: Staphylococcus Aureus Organism_taxid: 1280 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Fibrinogen Gamma-Chain Chain: C, D Fragment: C-Terminal Gamma-Chain Peptide Analog, Residues 425-437; Mutation: Yes		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
symmetry	Space Group: P 1	R_factor 0.21116 R_Free 0.27931
crystal cell	length a length b length c angle alpha angle beta angle gamma 35.427 61.836 81.777 85.44 81.84 82.45
method	X-Ray Diffraction	resolution	1.95 Å
Gene Ontology	Chain Function Process Component D, 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	A structural model of the Staphylococcus aureus ClfA-fibrinogen interaction opens new avenues for the design of anti-staphylococcal therapeutics., Ganesh VK, Rivera JJ, Smeds E, Ko YP, Bowden MG, Wann ER, Gurusiddappa S, Fitzgerald JR, Hook M, PLoS Pathog. 2008 Nov;4(11):e1000226. Epub 2008 Nov 28. PMID:19043557

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk] Biological Unit Coordinates (2vr3.pdb1.gz) 54 Kb Biological Unit Coordinates (2vr3.pdb2.gz) 55 Kb CSU: Contacts of Structural Units for 2VR3 Likely Quarternary Molecular Structure file(s) for 2VR3 Structure Factors (636 Kb) Retrieve 2VR3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VR3 from S2C, [Save to disk] Re-refined 2vr3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VR3 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 2VR3

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 2VR3, from MSDmotif at EBI Fold representative 2vr3 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vr3_A] [2vr3_B] [2vr3_C] [2vr3_D] SWISS-PROT database: [Q2G015] [P02679] Domain organization of [CLFA_STAA8] [FIBG_HUMAN] by SWISSPFAM Alignments of the sequence of 2VR3 with the sequences similar proteins can be viewed for 2VR3's classification [CLFA_STAA8] [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 [CLFA_STAA8] [FIBG_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2VR3

Community annotation for 2VR3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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