+Open data
-Basic information
Entry | Database: PDB / ID: 1w2k | ||||||
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Title | tf7a_4380 complex | ||||||
Components |
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Keywords | HYDROLASE / SERINE PROTEASE / BLOOD COAGULATION / GLYCOPROTEIN / PLASMA / VITAMIN K / CALCIUM-BINDING / GAMMA-CARBOXYGLUTAMIC ACID / CO-FACTOR / COAGULATION / ENZYME 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 / NGF-stimulated transcription / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / cytokine receptor activity / 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 / protein processing / phospholipid binding / cytokine-mediated signaling pathway / Golgi lumen / circadian rhythm / response to estrogen / positive regulation of angiogenesis / activation of cysteine-type endopeptidase activity involved in apoptotic process / blood coagulation / response to estradiol / collagen-containing extracellular matrix / protease binding / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Banner, D.W. / D'Arcy, A. / Groebke-Zbinden, K. / Ackermann, J. / Kirchhofer, D. / Ji, Y.-H. / Tschopp, T.B. / Wallbaum, S. / Weber, L. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2005 Title: Design of Selective Phenylglycine Amide Tissue Factor/Factor Viia Inhibitors Authors: Groebke-Zbinden, K. / Banner, D.W. / Ackermann, J. / D'Arcy, A. / Kirchhofer, D. / Ji, Y.-H. / Tschopp, T.B. / Wallbaum, S. / Weber, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w2k.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w2k.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 1w2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w2k_validation.pdf.gz | 826.9 KB | Display | wwPDB validaton report |
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Full document | 1w2k_full_validation.pdf.gz | 845.1 KB | Display | |
Data in XML | 1w2k_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 1w2k_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/1w2k ftp://data.pdbj.org/pub/pdb/validation_reports/w2/1w2k | HTTPS FTP |
-Related structure data
Related structure data | 1w0ySC 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 | THIS DESIGNATION IS BASED ON AN AUTOMATIC QUATERNARYSTRUCTURE DETERMINATION (PQS.EBI.AC.UK). |
-Components
-BLOOD COAGULATION FACTOR ... , 2 types, 2 molecules HL
#1: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: FACTOR VII HEAVY CHAIN, RESIDUES 213-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): KIDNEY CELLS (BHK) / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 16315.761 Da / Num. of mol.: 1 / Fragment: FACTOR VII HEAVY CHAIN, RESIDUES 61-202 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): KIDNEY CELLS (BHK) / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: P08709, coagulation factor VIIa |
-Protein , 1 types, 1 molecules T
#3: Protein | Mass: 23763.393 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 38-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13726 |
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-Sugars , 2 types, 2 molecules
#7: Sugar | ChemComp-FUC / |
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#8: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 383 molecules
#4: Chemical | ChemComp-380 / ( | ||||
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#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-CAC / | #9: Water | ChemComp-HOH / | |
-Details
Compound details | THE PEPTIDE GROUP LINKING RESIDUES 192 AND 193 OF THE HEAVY CHAIN OF FACTOR VIIA IS FLIPPED 180 ...THE PEPTIDE GROUP LINKING RESIDUES 192 AND 193 OF THE HEAVY CHAIN OF FACTOR VIIA IS FLIPPED 180 DEGREES FROM THE STANDARD ACTIVE CONFORMATI |
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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: 2.8 Å3/Da / Density % sol: 49.5 % |
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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 / Wavelength: 1.54182 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 16, 1996 / Details: SUPPER MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54182 Å / Relative weight: 1 |
Reflection | Resolution: 3→19.87 Å / Num. obs: 14546 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.15 |
Reflection shell | Resolution: 3→3.2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.02 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W0Y Resolution: 3→19.82 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE STRUCTURE WAS RE-REFINED FOR DEPOSITION, BASED ON 1W0Y.PDB
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10 /
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: F7_ALL_4380.TPX |