+Open data
-Basic information
Entry | Database: PDB / ID: 1ny2 | ||||||
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Title | Human alpha thrombin inhibited by RPPGF and hirugen | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / thrombosis / retro binding / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of blood coagulation / negative regulation of cell adhesion / cysteine-type endopeptidase inhibitor activity / 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 ...negative regulation of blood coagulation / negative regulation of cell adhesion / cysteine-type endopeptidase inhibitor activity / 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 / negative regulation of cytokine production involved in inflammatory response / positive regulation of collagen biosynthetic process / 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 / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / platelet alpha granule lumen / Regulation of Complement cascade / Post-translational protein phosphorylation / 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 / serine-type endopeptidase inhibitor activity / hormone activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / vasodilation / 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 / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / Platelet degranulation / heparin binding / positive regulation of cytosolic calcium ion concentration / regulation of cell shape / G alpha (i) signalling events / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / inflammatory response / positive regulation of protein phosphorylation / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Krishnan, R. / Tulinsky, A. / Schmaier, A.H. / Hasan, A.A. / Warnock, M. / Srikanth, S. / Mahdi, F. | ||||||
Citation | Journal: Am.J.Physiol.Heart Circ.Physiol. / Year: 2003 Title: Mechanisms of Arg-Pro-Pro-Gly-Phe inhibition of thrombin. Authors: Hasan, A.A. / Warnock, M. / Nieman, M. / Srikanth, S. / Mahdi, F. / Krishnan, R. / Tulinsky, A. / Schmaier, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ny2.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ny2.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ny2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/1ny2 ftp://data.pdbj.org/pub/pdb/validation_reports/ny/1ny2 | HTTPS FTP |
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-Related structure data
Related structure data | 1ditS S: Starting model for refinement |
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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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-Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: light chain A / Source method: isolated from a natural source / Details: alpha thrombin catalytic domain / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: heavy chain B / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
#3: Protein/peptide | Mass: 1363.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: P28504 |
#4: Protein/peptide | Mass: 573.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: P01042*PLUS |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.06 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, ammonium sulphate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 25K, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 11, 1997 / Details: yale mirrors |
Radiation | Monochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 23504 / Num. obs: 17158 / % possible obs: 73 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 2.1→2.3 Å / % possible all: 0.5 |
Reflection | *PLUS % possible obs: 73 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DIT Resolution: 2.3→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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