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- PDB-2vr3: Structural and Biochemical Characterization of Fibrinogen binding... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vr3 | ||||||
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Title | Structural and Biochemical Characterization of Fibrinogen binding to ClfA from Staphylocccus aureus | ||||||
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![]() | CELL ADHESION / PLATELET AGGREGATION / PEPTIDOGLYCAN-ANCHOR / STAPHYLOCOCCUS AUREUS / FIBRINOGEN GAMMA-CHAIN / SECRETED / CELL WALL / VIRULENCE / CLUMPING FACTOR | ||||||
Function / homology | ![]() aggregation of unicellular organisms / platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / platelet alpha granule / blood coagulation, fibrin clot formation / cell wall / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) ...aggregation of unicellular organisms / platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / platelet alpha granule / blood coagulation, fibrin clot formation / cell wall / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / fibronectin binding / : / protein secretion / protein polymerization / cellular response to interleukin-1 / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / cell adhesion molecule binding / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / Platelet degranulation / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / positive regulation of ERK1 and ERK2 cascade / blood microparticle / cell adhesion / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / structural molecule activity / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ganesh, V.K. / Rivera, J.J. / Smeds, E. / Bowden, M.G. / Wann, E.R. / Gurusidappa, S. / Fitzgerald, J.R. / Hook, M. | ||||||
![]() | ![]() Title: A Structural Model of the Staphylococcus Aureus Clfa-Fibrinogen Interaction Opens New Avenues for the Design of Anti-Staphylococcal Therapeutics. Authors: Ganesh, V.K. / Rivera, J.J. / Smeds, E. / Ko, Y.P. / Bowden, M.G. / Wann, E.R. / Gurusiddappa, S. / Fitzgerald, J.R. / Hook, M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.7 KB | Display | ![]() |
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PDB format | ![]() | 111.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.1 KB | Display | ![]() |
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Full document | ![]() | 463.8 KB | Display | |
Data in XML | ![]() | 30.7 KB | Display | |
Data in CIF | ![]() | 45.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n67S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35801.477 Da / Num. of mol.: 2 / Fragment: N2N3, RESIDUES 229-545 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ENGINEERED DISULFIDE BOND BETWEEN 327 AND 541 / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1276.424 Da / Num. of mol.: 2 Fragment: C-TERMINAL GAMMA-CHAIN PEPTIDE ANALOG, RESIDUES 425-437 Mutation: YES / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 327 TO CYS ENGINEERED RESIDUE IN CHAIN A, LYS 541 TO CYS ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 16-20% PEG 8000, 100MM SUCCINIC ACID PH 6.0 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→15 Å / Num. obs: 49456 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 2.7 / % possible all: 88.7 |
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Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1N67 Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU B: 3.108 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.927 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→15 Å
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