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Open data
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Basic information
Entry | Database: PDB / ID: 7v15 | ||||||
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Title | Factor XIa in Complex with Compound 2i | ||||||
![]() | Coagulation factor XIa light chain | ||||||
![]() | BLOOD CLOTTING / Hydrolase / SERINE PROTEASE / COAGULATION FACTOR | ||||||
Function / homology | ![]() coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shaffer, P.L. / Cedervall, P. / Milligan, C.M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Discovery of Potent and Orally Bioavailable Pyridine N-Oxide-Based Factor XIa Inhibitors through Exploiting Nonclassical Interactions. Authors: Xu, G. / Liu, Z. / Wang, X. / Lu, T. / DesJarlais, R.L. / Thieu, T. / Zhang, J. / Devine, Z.H. / Du, F. / Li, Q. / Milligan, C.M. / Shaffer, P. / Cedervall, P.E. / Spurlino, J.C. / Stratton, ...Authors: Xu, G. / Liu, Z. / Wang, X. / Lu, T. / DesJarlais, R.L. / Thieu, T. / Zhang, J. / Devine, Z.H. / Du, F. / Li, Q. / Milligan, C.M. / Shaffer, P. / Cedervall, P.E. / Spurlino, J.C. / Stratton, C.F. / Pietrak, B. / Szewczuk, L.M. / Wong, V. / Steele, R.A. / Bruinzeel, W. / Chintala, M. / Silva, J. / Gaul, M.D. / Macielag, M.J. / Nargund, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.3 KB | Display | ![]() |
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PDB format | ![]() | 85.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 789.2 KB | Display | ![]() |
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Full document | ![]() | 790.3 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7v0zC ![]() 7v10C ![]() 7v11C ![]() 7v12C ![]() 7v13C ![]() 7v14C ![]() 7v16C ![]() 7v17C ![]() 7v18C ![]() 3sosS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 26856.496 Da / Num. of mol.: 1 / Mutation: C500S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-OSX / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 24% PEG 4000, 100mM Na Citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.679→44.583 Å / Num. obs: 26775 / % possible obs: 95.36 % / Redundancy: 6.2 % / Biso Wilson estimate: 26.47 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.679→1.739 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2764 / CC1/2: 0.88 / Rpim(I) all: 0.338 / Rrim(I) all: 0.885 / % possible all: 99.64 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SOS Resolution: 1.679→44.583 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.48 / Stereochemistry target values: ML
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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 max: 99.06 Å2 / Biso mean: 35.8272 Å2 / Biso min: 17.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.679→44.583 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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