+Open data
-Basic information
Entry | Database: PDB / ID: 2bok | ||||||
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Title | Factor Xa - cation | ||||||
Components | (COAGULATION FACTOR X) x 2 | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / COAGULATION FACTOR / CATION / INHIBITOR / EGF- LIKE DOMAIN / PLASMA / PROTEASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Morgenthaler, M. / Schaerer, K. / Paulini, R. / Obst-Sander, U. / Banner, D.W. / Schlatter, D. / Benz, J. / Stihle, M. / Diederich, F. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2005 Title: Quantification of Cation-Pi Interactions in Protein-Ligand Complexes: Crystal-Structure Analysis of Factor Xa Bound to a Quaternary Ammonium Ion Ligand Authors: Scharer, K. / Morgenthaler, M. / Paulini, R. / Obst-Sander, U. / Banner, D.W. / Schlatter, D. / Benz, J. / Stihle, M. / Diederich, F. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bok.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bok.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 2bok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bok_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 2bok_full_validation.pdf.gz | 457.5 KB | Display | |
Data in XML | 2bok_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 2bok_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/2bok ftp://data.pdbj.org/pub/pdb/validation_reports/bo/2bok | HTTPS FTP |
-Related structure data
Related structure data | 1c5mS 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: 27172.980 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 234-475 / Mutation: YES 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: EGF2 DOMAIN, 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 |
#3: Chemical | ChemComp-784 / [ |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34 % |
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Crystal grow | pH: 5.5 / Details: pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54182 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 14, 2004 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54182 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→20 Å / Num. obs: 32725 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.62→1.71 Å / Redundancy: 4.77 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.33 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C5M Resolution: 1.64→51.03 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.498 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.113 / 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: 20.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→51.03 Å
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Refine LS restraints |
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