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- PDB-3s9c: Russell's viper venom serine proteinase, RVV-V in complex with th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3s9c | |||||||||
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Title | Russell's viper venom serine proteinase, RVV-V in complex with the fragment (residues 1533-1546) of human factor V | |||||||||
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![]() | HYDROLASE / serine proteinase / double six-stranded beta-barrels / glycosylation | |||||||||
Function / homology | ![]() snake venom factor V activator / response to vitamin K / platelet alpha granule / Cargo concentration in the ER / blood circulation / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Common Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen ...snake venom factor V activator / response to vitamin K / platelet alpha granule / Cargo concentration in the ER / blood circulation / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Common Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / extracellular vesicle / Platelet degranulation / signaling receptor activity / toxin activity / copper ion binding / endoplasmic reticulum lumen / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nakayama, D. / Ben Ammar, Y. / Takeda, S. | |||||||||
![]() | ![]() Title: Structural basis of coagulation factor V recognition for cleavage by RVV-V Authors: Nakayama, D. / Ben Ammar, Y. / Miyata, T. / Takeda, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Crystallization and preliminary X-ray crystallographic analysis of blood coagulation factor V-activating proteinase (RVV-V) from Russell's viper venom Authors: Nakayama, D. / Ben Ammar, Y. / Takeda, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.8 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.6 KB | Display | ![]() |
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Full document | ![]() | 802.6 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s9aSC ![]() 3s9bC ![]() 3sbkC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 25960.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Tissue: venom / References: UniProt: P18965, snake venom factor V activator |
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#2: Protein/peptide | Mass: 1665.806 Da / Num. of mol.: 1 / Fragment: UNP residues 1561-1574 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) ![]() |
-Sugars , 3 types, 3 molecules ![](data/chem/img/BGC.gif)
![](data/chem/img/GLC.gif)
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#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-BGC / |
#5: Sugar | ChemComp-GLC / |
-Non-polymers , 3 types, 203 molecules ![](data/chem/img/ACT.gif)
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![](data/chem/img/HOH.gif)
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#6: Chemical | ChemComp-ACT / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE RESIDUE NUMBERING IS NOT SEQUENTIAL. THE RESIDUE NUMBERING IS BASED ON THE TOPOLOGICAL ...THE RESIDUE NUMBERING IS NOT SEQUENTIAL |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20% PEG 3350, 0.2M zinc acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 13, 2009 / Details: mirrors |
Radiation | Monochromator: Rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 24272 / Num. obs: 24029 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 46.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 6.9 / Num. unique all: 2213 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3S9A Resolution: 1.8→29.21 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1637135.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.5738 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→29.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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