+Open data
-Basic information
Entry | Database: PDB / ID: 5voe | |||||||||
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Title | DesGla-XaS195A Bound to Aptamer 11F7t | |||||||||
Components |
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Keywords | HYDROLASE/RNA / Serine Protease / Blood Coagulation / Aptamer / Inhibitor / HYDROLASE-RNA complex | |||||||||
Function / homology | Function and homology information coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Gunaratne, R. / Kumar, S. / Frederiksen, J.W. / Stayrook, S. / Lohrmann, J.L. / Perry, K. / Chabata, C.V. / Thalji, N.K. / Ho, M.D. / Arepally, G. ...Gunaratne, R. / Kumar, S. / Frederiksen, J.W. / Stayrook, S. / Lohrmann, J.L. / Perry, K. / Chabata, C.V. / Thalji, N.K. / Ho, M.D. / Arepally, G. / Camire, R.M. / Krishnaswamy, S.K. / Sullenger, B.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat. Biotechnol. / Year: 2018 Title: Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass. Authors: Gunaratne, R. / Kumar, S. / Frederiksen, J.W. / Stayrook, S. / Lohrmann, J.L. / Perry, K. / Bompiani, K.M. / Chabata, C.V. / Thalji, N.K. / Ho, M.D. / Arepally, G. / Camire, R.M. / ...Authors: Gunaratne, R. / Kumar, S. / Frederiksen, J.W. / Stayrook, S. / Lohrmann, J.L. / Perry, K. / Bompiani, K.M. / Chabata, C.V. / Thalji, N.K. / Ho, M.D. / Arepally, G. / Camire, R.M. / Krishnaswamy, S. / Sullenger, B.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5voe.cif.gz | 176.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5voe.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 5voe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5voe_validation.pdf.gz | 475.3 KB | Display | wwPDB validaton report |
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Full document | 5voe_full_validation.pdf.gz | 495 KB | Display | |
Data in XML | 5voe_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 5voe_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/5voe ftp://data.pdbj.org/pub/pdb/validation_reports/vo/5voe | HTTPS FTP |
-Related structure data
Related structure data | 5vofC 2y5gS S: Starting model for refinement C: citing same article (ref.) |
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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
-Coagulation factor ... , 2 types, 2 molecules HL
#1: Protein | Mass: 26330.000 Da / Num. of mol.: 1 / Fragment: residues 235-467 / Mutation: S419A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F10 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa |
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#2: Protein | Mass: 5460.055 Da / Num. of mol.: 1 / Fragment: residues 128-178 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F10 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa |
-RNA chain , 1 types, 1 molecules A
#3: RNA chain | Mass: 11538.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 163 molecules
#4: Chemical | ChemComp-NA / | ||
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#5: Chemical | ChemComp-CA / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Bicine, 0.1 M Tris base, 0.1 M Carboxylic Acids, 10% PEG 20,000, 20% PEG 500 monomethyl ester |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→82.3 Å / Num. obs: 38141 / % possible obs: 97.04 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2→2.072 Å / Rmerge(I) obs: 1.204 / Num. unique obs: 3725 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Y5G Resolution: 2→82.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.875 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.368 Å2
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Refinement step | Cycle: 1 / Resolution: 2→82.3 Å
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