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Yorodumi- PDB-2xc5: Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xc5 | ||||||
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Title | Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor | ||||||
Components |
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Keywords | BLOOD CLOTTING / COAGULATION / COAGULATION FACTOR / HYDROLASE / HYDROXYLATION / SERINE PROTEASE / ZYMOGEN | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Banner, D.W. / Benz, J. / Schlatter, D. / Anselm, L. / Haap, W. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: Discovery of a Factor Xa Inhibitor (3R,4R)-1-(2,2-Difluoro-Ethyl)-Pyrrolidine-3,4-Dicarboxylic Acid 3-[(5-Chloro-Pyridin-2-Yl)-Amide] 4-{[2-Fluoro-4-(2-Oxo-2H-Pyridin-1-Yl)-Phenyl]-Amide} as a Clinical Candidate. Authors: Anselm, L. / Banner, D.W. / Benz, J. / Groebke Zbinden, K. / Himber, J. / Hilpert, H. / Huber, W. / Kuhn, B. / Mary, J.L. / Otteneder, M.B. / Panday, N. / Ricklin, F. / Stahl, M. / Thomi, S. / Haap, W. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xc5.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xc5.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xc5_validation.pdf.gz | 787.5 KB | Display | wwPDB validaton report |
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Full document | 2xc5_full_validation.pdf.gz | 791.5 KB | Display | |
Data in XML | 2xc5_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2xc5_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/2xc5 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/2xc5 | HTTPS FTP |
-Related structure data
Related structure data | 2xbvC 2xbwC 2xbxC 2xbyC 2xc0C 2xc4C 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
-Protein , 2 types, 2 molecules AL
#1: Protein | Mass: 27201.061 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 235-475 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00742, coagulation factor Xa |
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#2: Protein | Mass: 6060.816 Da / Num. of mol.: 1 / Fragment: LIGHTCHAIN, RESIDUES 126-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00742, coagulation factor Xa |
-Non-polymers , 4 types, 178 molecules
#3: Chemical | ChemComp-OYJ / ( |
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#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-NA / |
#6: 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: 2.31 Å3/Da / Density % sol: 46.7 % / Description: LOW COMPLETENESS DUE TO ICE RING EXCLUSION |
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Crystal grow | pH: 6.5 / Details: PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→20 Å / Num. obs: 28575 / % possible obs: 83 % / Observed criterion σ(I): -3 / Redundancy: 9.21 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.08 |
Reflection shell | Resolution: 1.66→1.76 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.56 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN HOUSE Resolution: 1.7→74.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.352 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.951 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→74.94 Å
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