+Open data
-Basic information
Entry | Database: PDB / ID: 2j2u | ||||||
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Title | CRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX | ||||||
Components |
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Keywords | HYDROLASE / GAMMA- CARBOXYGLUTAMIC ACID / SERINE PROTEASE / EGF-LIKE DOMAIN / BLOOD COAGULATION / POLYMORPHISM / GLYCOPROTEIN / HYDROXYLATION / GAMMA-CARBOXYGLUTAMIC ACID / CALCIUM / ZYMOGEN / COMPLEX / 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 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 | Senger, S. / Convery, M.A. / Chan, C. / Watson, N.S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Arylsulfonamides: A Study of the Relationship between Activity and Conformational Preferences for a Series of Factor Xa Inhibitors. Authors: Senger, S. / Convery, M.A. / Chan, C. / Watson, N.S. | ||||||
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 | 2j2u.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j2u.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 2j2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/2j2u ftp://data.pdbj.org/pub/pdb/validation_reports/j2/2j2u | HTTPS FTP |
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-Related structure data
Related structure data | 2j34C 2j38C 1ezqS 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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Details | FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350 |
-Components
#1: Protein | Mass: 28550.596 Da / Num. of mol.: 1 / Fragment: ACTIVATED DESGLA, RESIDUES 235-488 / Source method: isolated from a natural source Details: PURCHASED FROM ENZYM RESEARCH LABS. ISOLATED FROM HUMAN BLOOD Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00742, coagulation factor Xa |
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#2: Protein | Mass: 15210.793 Da / Num. of mol.: 1 / Fragment: ACTIVATED DESGLA, RESIDUES 46-179 / Source method: isolated from a natural source Details: PURCHASED FROM ENZYM RESEARCH LABS. ISOLATED FROM HUMAN BLOOD Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00742, coagulation factor Xa |
#3: Chemical | ChemComp-GSQ / |
#4: Water | ChemComp-HOH / |
Sequence details | SOME RESIDUES IN CHAIN ARE NOT SEEN IN THE ELECTRON DENSITY. SEQUENCE DATABASE RESIDUES 1-45 (THE ...SOME RESIDUES IN CHAIN ARE NOT SEEN IN THE ELECTRON DENSITY. SEQUENCE DATABASE RESIDUES 1-45 (THE GLA DOMAIN) WERE BIOCHEMICA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.15 % |
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Crystal grow | pH: 5.85 / Details: 18% PEG6K, 50MM MES PH 5.85, 5MM CACL2, 50MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Date: Nov 30, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 144420 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.54 % / Rmerge(I) obs: 0.05 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.52 % / Rmerge(I) obs: 0.38 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EZQ Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.246 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.143 / 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: 32.97 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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