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- PDB-6xfq: Structure of a novel antithrombotic agent Agkisacucetin in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xfq | ||||||
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Title | Structure of a novel antithrombotic agent Agkisacucetin in complex with the platelet glycoprotein Ib receptor | ||||||
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![]() | STRUCTURAL PROTEIN / complex / GPIb | ||||||
Function / homology | ![]() thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / regulation of blood coagulation / Platelet Aggregation (Plug Formation) / release of sequestered calcium ion into cytosol / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / extracellular matrix / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell morphogenesis / platelet activation / blood coagulation / toxin activity / cell surface receptor signaling pathway / cell adhesion / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wang, J. / Gao, Y.X. / Ke, J.Y. / Zhu, Z.L. / Niu, L.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a novel antithrombotic agent Agkisacucetin in complex with the platelet glycoprotein Ib receptor Authors: Wang, J. / Gao, Y.X. / Ke, J.Y. / Zhu, Z.L. / Niu, L.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.4 KB | Display | ![]() |
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PDB format | ![]() | 89.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.1 KB | Display | ![]() |
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Full document | ![]() | 463.8 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 28.3 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 34010.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 17334.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() |
#3: Protein | Mass: 17258.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.29 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 15% PEG4000, 0.1M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→58.1 Å / Num. obs: 11456 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 115.46 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.057 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.3→3.56 Å / Redundancy: 8.6 % / Num. unique obs: 2290 / CC1/2: 0.918 / Rpim(I) all: 0.674 / % possible all: 99.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P9A, 3UBU Resolution: 3.3→51.34 Å / SU ML: 0.546 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 44.5898 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 162.83 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→51.34 Å
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Refine LS restraints |
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LS refinement shell |
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