+Open data
-Basic information
Entry | Database: PDB / ID: 1dx5 | |||||||||
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Title | Crystal structure of the thrombin-thrombomodulin complex | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / EGF-LIKE DOMAINS / ANTICOAGULANT COMPLEX / ANTIFIBRINOLYTIC COMPLEX / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information blood coagulation, common pathway / negative regulation of blood coagulation / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity ...blood coagulation, common pathway / negative regulation of blood coagulation / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / response to X-ray / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / 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 / response to cAMP / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / female pregnancy / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / transmembrane signaling receptor activity / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor activity / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / response to lipopolysaccharide / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Fuentes-Prior, P. / Iwanaga, Y. / Huber, R. / Pagila, R. / Rumennik, G. / Seto, M. / Morser, J. / Light, D.R. / Bode, W. | |||||||||
Citation | Journal: Nature / Year: 2000 Title: Structural Basis for the Anticoagulant Activity of the Thrombin-Thrombomodulin Complex Authors: Fuentes-Prior, P. / Iwanaga, Y. / Huber, R. / Pagila, R. / Rumennik, G. / Seto, M. / Morser, J. / Light, D.R. / Bode, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dx5.cif.gz | 353.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dx5.ent.gz | 291 KB | Display | PDB format |
PDBx/mmJSON format | 1dx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dx5 ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dx5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules IJKLMNOP
#2: Protein | Mass: 12691.090 Da / Num. of mol.: 4 / Fragment: EGF-LIKE DOMAINS 4 - 6 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ENZYMATICALLY DEGLYCOSYLATED (PNGASE F) / Source: (gene. exp.) Homo sapiens (human) / Tissue: ENDOTHELIUM / Gene: THBD, THRM / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P07204 #3: Protein | Mass: 29792.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURIFIED FROM FROZEN PLASMA / Source: (natural) Homo sapiens (human) / Secretion: BLOOD PLASMA / References: UniProt: P00734, thrombin |
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-Protein/peptide / Sugars , 2 types, 8 molecules ABCD
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURIFIED FROM FROZEN PLASMA / Source: (natural) Homo sapiens (human) / Secretion: BLOOD PLASMA / References: UniProt: P00734, thrombin #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 848 molecules
#4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-NA / #8: Chemical | ChemComp-0GJ / #9: Water | ChemComp-HOH / | |
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-Details
Compound details | THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG- CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT ...THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG- CHLOROMETH |
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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: 2.64 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.105 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.105 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→43.85 Å / Num. obs: 670680 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 15.55 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 3.87 / Rsym value: 0.169 / % possible all: 99.7 |
Reflection | *PLUS Num. obs: 99777 |
Reflection shell | *PLUS Rmerge(I) obs: 0.169 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: THROMBIN-PPACK Resolution: 2.3→10 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Details: RESIDUES 14L-15 NOT SEEN IN THE DENSITY MAP
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |