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Yorodumi- PDB-6hhc: Allosteric Inhibition as a new mode of Action for BAY 1213790, a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hhc | ||||||
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Title | Allosteric Inhibition as a new mode of Action for BAY 1213790, a Neutralizing Antibody Targeting the Activated form of Coagulation Factor XI | ||||||
Components |
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Keywords | BLOOD CLOTTING / FXIA ANTIBODY FAB / BLOOD CLOTTING-IMMUNE COMPLEX | ||||||
Function / homology | Function and homology information 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Schaefer, M. / Buchmueller, A. / Dittmer, F. / Strassburger, J. / Wilmen, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Allosteric Inhibition as a New Mode of Action for BAY 1213790, a Neutralizing Antibody Targeting the Activated Form of Coagulation Factor XI. Authors: Schaefer, M. / Buchmueller, A. / Dittmer, F. / Strassburger, J. / Wilmen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hhc.cif.gz | 262.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hhc.ent.gz | 212.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/6hhc ftp://data.pdbj.org/pub/pdb/validation_reports/hh/6hhc | HTTPS FTP |
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-Related structure data
Related structure data | 3gjeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23496.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||
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#2: Antibody | Mass: 23935.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||
#3: Protein | Mass: 26856.496 Da / Num. of mol.: 1 / Mutation: C500S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Homo sapiens (human) / References: UniProt: P03951, coagulation factor XIa | ||
#4: Chemical | #5: Chemical | ChemComp-DMS / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.09 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.5 / Details: 20 mM Tris-HCl pH 7.5,75 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91832 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: May 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91832 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→99 Å / Num. obs: 23127 / % possible obs: 99.8 % / Redundancy: 4.2 % / Net I/σ(I): 9.41 |
Reflection shell | Resolution: 2.7→2.86 Å |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GJE Resolution: 2.7→92.95 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.815 / SU B: 36.909 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.077 / ESU R Free: 0.415 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.08 Å2 / Biso mean: 38.936 Å2 / Biso min: 16.36 Å2
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Refinement step | Cycle: final / Resolution: 2.7→92.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.698→2.768 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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