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- PDB-1uex: Crystal structure of von Willebrand Factor A1 domain complexed wi... -
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Basic information
Entry | Database: PDB / ID: 1uex | ||||||
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Title | Crystal structure of von Willebrand Factor A1 domain complexed with snake venom bitiscetin | ||||||
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![]() | TOXIN/BLOOD CLOTTING / C-type lectin heterodimer / TOXIN-BLOOD CLOTTING COMPLEX | ||||||
Function / homology | ![]() Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / 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 / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / signaling receptor activity / toxin activity / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maita, N. / Nishio, K. / Nishimoto, E. / Matsui, T. / Shikamoto, Y. / Morita, T. / Sadler, J.E. / Mizuno, H. | ||||||
![]() | ![]() Title: Crystal structure of von Willebrand factor A1 domain complexed with snake venom, bitiscetin. Insight into glycoprotein Ibalpha binding mechanism induced by snake venom proteins. Authors: Maita, N. / Nishio, K. / Nishimoto, E. / Matsui, T. / Shikamoto, Y. / Morita, T. / Sadler, J.E. / Mizuno, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.8 KB | Display | ![]() |
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PDB format | ![]() | 79.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.6 KB | Display | ![]() |
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Full document | ![]() | 455.8 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 14953.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 14822.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 23889.627 Da / Num. of mol.: 1 / Fragment: A1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 39.8 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 10% PEG 6000, 2% PEG-MME 550, 5% MPD, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 283K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 13, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→30 Å / Num. obs: 9672 / % possible obs: 91.6 % / Redundancy: 5.6 % / Rsym value: 0.107 |
Reflection shell | Resolution: 2.85→2.99 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.31 / % possible all: 91.6 |
Reflection | *PLUS Num. obs: 9055 / Num. measured all: 51631 / Rmerge(I) obs: 0.107 |
Reflection shell | *PLUS % possible obs: 91.6 % / Num. unique obs: 1456 / Num. measured obs: 8285 / Rmerge(I) obs: 0.311 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JWI and 1AUQ Resolution: 2.85→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.85→20 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 12 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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