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- PDB-2xby: Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xby | ||||||
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Title | Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor | ||||||
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![]() | BLOOD CLOTTING / COAGULATION / COAGULATION FACTOR / HYDROLASE / HYDROXYLATION / SERINE PROTEASE / ZYMOGEN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Banner, D.W. / Benz, J. / Schlatter, D. / Thomi, S. / Haap, W. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.1 KB | Display | ![]() |
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PDB format | ![]() | 57.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 770.3 KB | Display | ![]() |
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Full document | ![]() | 775.2 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xbvC ![]() 2xbwC ![]() 2xbxC ![]() 2xc0C ![]() 2xc4C ![]() 2xc5C C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() |
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#2: Protein | Mass: 6060.816 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 126-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 231 molecules ![](data/chem/img/63C.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-63C / ( |
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#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE |
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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: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 24, 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: 2.02→20 Å / Num. obs: 19557 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.14 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.02→2.15 Å / Redundancy: 5.86 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.73 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: IN HOUSE STRUCTURE Resolution: 2.02→14.85 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 408996.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 92.2923 Å2 / ksol: 0.308618 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.02→14.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.15 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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