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Yorodumi- PDB-5alb: Ticagrelor antidote candidate MEDI2452 in complex with ticagrelor -
+Open data
-Basic information
Entry | Database: PDB / ID: 5alb | ||||||
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Title | Ticagrelor antidote candidate MEDI2452 in complex with ticagrelor | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIBODY FRAGMENT / ANTIDOTE / DRUG | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Ticagrelor Function and homology information | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Buchanan, A. / Newton, P. / Pehrsson, S. / Inghardt, T. / Antonsson, T. / Svensson, P. / Sjogren, T. / Oster, L. / Janefeldt, A. / Sandinge, A. ...Buchanan, A. / Newton, P. / Pehrsson, S. / Inghardt, T. / Antonsson, T. / Svensson, P. / Sjogren, T. / Oster, L. / Janefeldt, A. / Sandinge, A. / Keyes, F. / Austin, M. / Spooner, J. / Penney, M. / Howells, G. / Vaughan, T. / Nylander, S. | ||||||
Citation | Journal: Blood / Year: 2015 Title: Structural and Functional Characterisation of a Specific Antidote for Ticagrelor. Authors: Buchanan, A. / Newton, P. / Pehrsson, S. / Inghardt, T. / Antonsson, T. / Svensson, P. / Sjogren, T. / Oster, L. / Janefeldt, A. / Sandinge, A. / Keyes, F. / Austin, M. / Spooner, J. / ...Authors: Buchanan, A. / Newton, P. / Pehrsson, S. / Inghardt, T. / Antonsson, T. / Svensson, P. / Sjogren, T. / Oster, L. / Janefeldt, A. / Sandinge, A. / Keyes, F. / Austin, M. / Spooner, J. / Gennemark, P. / Penney, M. / Howells, G. / Vaughan, T. / Nylander, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5alb.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5alb.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 5alb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5alb_validation.pdf.gz | 741.3 KB | Display | wwPDB validaton report |
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Full document | 5alb_full_validation.pdf.gz | 745.3 KB | Display | |
Data in XML | 5alb_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 5alb_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/5alb ftp://data.pdbj.org/pub/pdb/validation_reports/al/5alb | HTTPS FTP |
-Related structure data
Related structure data | 5alcC 1aqkS C: citing same article (ref.) 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: 24705.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) |
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#2: Antibody | Mass: 22786.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) |
#3: Chemical | ChemComp-TIQ / |
#4: Water | ChemComp-HOH / |
Sequence details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.36 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Jun 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→44.4 Å / Num. obs: 36570 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 46.98 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.1 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AQK Resolution: 2.16→41 Å / Cor.coef. Fo:Fc: 0.9187 / Cor.coef. Fo:Fc free: 0.8816 / SU R Cruickshank DPI: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.223 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.193 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 44.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.305 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.16→41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.16→2.24 Å / Total num. of bins used: 14
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