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Yorodumi- PDB-1z6j: Crystal Structure of a ternary complex of Factor VIIa/Tissue Fact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z6j | ||||||
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Title | Crystal Structure of a ternary complex of Factor VIIa/Tissue Factor/Pyrazinone Inhibitor | ||||||
Components |
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Keywords | HYDROLASE / Blood coagulation / serine protease / thrombosis / gla / pyrazinone / benzamidine / tissue factor / cofactor / enzyme inhibitor complex | ||||||
Function / homology | Function and homology information activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway ...activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / positive regulation of leukocyte chemotaxis / NGF-stimulated transcription / response to cholesterol / response to growth hormone / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of interleukin-8 production / circadian rhythm / protein processing / phospholipid binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / cytokine-mediated signaling pathway / Golgi lumen / response to estrogen / positive regulation of angiogenesis / blood coagulation / response to estradiol / protease binding / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of gene expression / cell surface / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Schweitzer, B.A. / Neumann, W.L. / Rahman, H.K. / Kusturin, C.L. / Sample, K.R. / Poda, G.I. / Kurumbail, R.G. / Stevens, A.M. / Stegeman, R.A. / Stallings, W.C. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2005 Title: Structure-based design and synthesis of pyrazinones containing novel P1 'side pocket' moieties as inhibitors of TF/VIIa. Authors: Schweitzer, B.A. / Neumann, W.L. / Rahman, H.K. / Kusturin, C.L. / Sample, K.R. / Poda, G.I. / Kurumbail, R.G. / Stevens, A.M. / Stegeman, R.A. / Stallings, W.C. / South, M.S. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 2003 Title: Structure-based design of pyrazinone antithrombotics as selective inhibitors of the tissue factor VIIa complex Authors: South, M.S. / Case, B.L. / Wood, R.S. / Jones, D.E. / Hayes, M.J. / Girard, T.J. / LaChance, R.M. / Nicholson, N.S. / Clare, M. / Stevens, A.M. / Stegeman, R.A. / Stallings, W.C. / Kurumbail, R.G. / Parlow, J.J. #2: Journal: J.Med.Chem. / Year: 2003 Title: Polymer-assisted solution-phase library synthesis and crystal structure of alpha-ketothiazoles as tissue factor VIIa inhibitors Authors: Parlow, J.J. / Dice, T.A. / LaChance, R.M. / Girard, T.J. / Stevens, A.M. / Stegeman, R.A. / Stallings, W.C. / Kurumbail, R.G. / South, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z6j.cif.gz | 140 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z6j.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 1z6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z6j_validation.pdf.gz | 816.4 KB | Display | wwPDB validaton report |
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Full document | 1z6j_full_validation.pdf.gz | 838.1 KB | Display | |
Data in XML | 1z6j_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 1z6j_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/1z6j ftp://data.pdbj.org/pub/pdb/validation_reports/z6/1z6j | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Coagulation factor ... , 2 types, 2 molecules LH
#1: Protein | Mass: 16359.772 Da / Num. of mol.: 1 / Fragment: Light Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Organ (production host): Kidney / Production host: Cricetinae (hamsters) / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: Heavy Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Organ (production host): kidney / Production host: Cricetinae (hamsters) / References: UniProt: P08709, coagulation factor VIIa |
-Protein , 1 types, 1 molecules T
#3: Protein | Mass: 23820.443 Da / Num. of mol.: 1 / Fragment: Residues 33-243 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / Production host: Escherichia coli (E. coli) / References: UniProt: P13726 |
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-Non-polymers , 4 types, 393 molecules
#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-PY3 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 50 mM citrate, 16-24% PEG 4K, 150 mM MgCl2, pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 23, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 47697 / Num. obs: 46245 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Χ2: 0.992 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2→2.07 Å / % possible obs: 94.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 4563 / Num. unique all: 4563 / Rsym value: 0.38 / Χ2: 0.823 / % possible all: 94.3 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→20 Å / Isotropic thermal model: isotropic, restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Bulksolvent correction applied
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Displacement parameters | Biso mean: 25.848 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell |
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