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Yorodumi- PDB-2w3i: Crystal Structure of FXa in complex with 4,4-disubstituted pyrrol... -
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-Basic information
Entry | Database: PDB / ID: 2w3i | ||||||
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Title | Crystal Structure of FXa in complex with 4,4-disubstituted pyrrolidine-1,2-dicarboxamide inhibitor 2 | ||||||
Components |
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Keywords | HYDROLASE / DRUG DESIGN / GLYCOPROTEIN / HYDROXYLATION / BLOOD CLOTTING / SERINE PROTEASE / EGF-LIKE DOMAIN / FXA COAGULATION FACTOR INHIBITOR / ZYMOGEN / PROTEASE / SECRETED / BLOOD COAGULATION / GAMMA-CARBOXYGLUTAMIC ACID / CLEAVAGE ON PAIR OF BASIC RESIDUES | ||||||
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 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 ...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 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: 1.9 Å | ||||||
Authors | Zhang, E. / Mochalkin, I. / Casimiro-Garcia, A. / Van Huis, C.A. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2009 Title: Exploration of 4,4-Disubstituted Pyrrolidine-1,2-Dicarboxamides as Potent, Orally Active Factor Xa Inhibitors with Extended Duration of Action. Authors: Van Huis, C.A. / Casimiro-Garcia, A. / Bigge, C.F. / Cody, W.L. / Dudley, D.A. / Filipski, K.J. / Heemstra, R.J. / Kohrt, J.T. / Leadley, R.J.J. / Narasimhan, L.S. / Mcclanahan, T. / ...Authors: Van Huis, C.A. / Casimiro-Garcia, A. / Bigge, C.F. / Cody, W.L. / Dudley, D.A. / Filipski, K.J. / Heemstra, R.J. / Kohrt, J.T. / Leadley, R.J.J. / Narasimhan, L.S. / Mcclanahan, T. / Mochalkin, I. / Pamment, M. / Peterson, J.T. / Sahasrabudhe, V. / Schaum, R.P. / Edmunds, J.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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 | 2w3i.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w3i.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 2w3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/2w3i ftp://data.pdbj.org/pub/pdb/validation_reports/w3/2w3i | HTTPS FTP |
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-Related structure data
Related structure data | 2w3kC 2phbS 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: Protein | Mass: 26447.104 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 235-468 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: 5460.055 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 128-178 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 |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-L1C / ( |
#5: 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: 2.34 Å3/Da / Density % sol: 46.91 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 24375 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 4.89 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.08 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.46 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PHB Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.547 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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