|Entry||Database: PDB / ID: 1lhg|
|Title||HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BOROORNITHINE-OH|
|Keywords||COMPLEX (SERINE PROTEASE/INHIBITOR) / BLOOD COAGULATION / PLASMA / CALCIUM-BINDING / GLYCOPROTEIN / DUPLICATION / VITAMIN K / ZYMOGEN / GAMMA-CARBOXYGLUTAMIC ACID / ACUTE PHASE / LIVER / HYDROLASE / SERINE PROTEASE / KRINGLE / DISEASE MUTATION / COMPLEX (SERINE PROTEASE-INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) complex|
|Function / homology|
Function and homology information
positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / cytolysis by host of symbiont cells / thrombin / regulation of blood coagulation / blood coagulation, common pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / cytolysis by host of symbiont cells / thrombin / regulation of blood coagulation / blood coagulation, common pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of fibrinolysis / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / 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 / Peptide ligand-binding receptors / regulation of cytosolic calcium ion concentration / positive regulation of receptor signaling pathway via JAK-STAT / zymogen activation / positive regulation of release of sequestered calcium ion into cytosol / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Thrombin signalling through proteinase activated receptors (PARs) / serine-type endopeptidase complex / Regulation of Complement cascade / lipopolysaccharide binding / acute-phase response / Cell surface interactions at the vascular wall / negative regulation of proteolysis / growth factor activity / response to wounding / positive regulation of protein localization to nucleus / platelet activation / Golgi lumen / positive regulation of reactive oxygen species metabolic process / G alpha (q) signalling events / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / positive regulation of phosphatidylinositol 3-kinase signaling / heparin binding / positive regulation of cell growth / regulation of cell shape / collagen-containing extracellular matrix / blood microparticle / antimicrobial humoral immune response mediated by antimicrobial peptide / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / proteolysis / signaling receptor binding / serine-type endopeptidase activity / endoplasmic reticulum lumen / calcium ion binding / positive regulation of cell population proliferation / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin light chain / Prothrombin/thrombin / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle domain / Kringle, conserved site / Kringle domain signature. / Kringle domain profile. / Kringle superfamily ...Thrombin light chain / Prothrombin/thrombin / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle domain / Kringle, conserved site / Kringle domain signature. / Kringle domain profile. / Kringle superfamily / Kringle / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
AC-(D)PHE-PRO-BOROHOMOORNITHINE-OH / Prothrombin
Similarity search - Component
|Biological species||Hirudo medicinalis (medicinal leech)|
Homo sapiens (human)
|Method||X-RAY DIFFRACTION / Resolution: 2.25 Å|
|Authors||Weber, P.C. / Lee, S.L. / Lewandowski, F.A. / Schadt, M.C. / Chang, C.H. / Kettner, C.A.|
|Citation||Journal: Biochemistry / Year: 1995|
Title: Kinetic and crystallographic studies of thrombin with Ac-(D)Phe-Pro-boroArg-OH and its lysine, amidine, homolysine, and ornithine analogs.
Authors: Weber, P.C. / Lee, S.L. / Lewandowski, F.A. / Schadt, M.C. / Chang, C.W. / Kettner, C.A.
|Structure viewer||Molecule: |
Downloads & links
|#1: Protein/peptide|| |
Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00734, thrombin
|#2: Protein|| |
Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00734, thrombin
|#3: Protein/peptide|| |
Mass: 1468.517 Da / Num. of mol.: 1 / Fragment: RESIDUES 54 - 65
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech)
|#4: Chemical|| ChemComp-DI5 / |
|#5: Water|| ChemComp-HOH / |
|Compound details||THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER|
|Sequence details||CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT ...CHYMOTRYPS|
|Experiment||Method: X-RAY DIFFRACTION|
|Crystal||Density Matthews: 2.55 Å3/Da / Density % sol: 51.85 %|
*PLUSpH: 7.3 / Method: vapor diffusion, hanging drop / Details: Skrzypczak, J., (1991) J. Mol. Biol., 221, 1379.
|Components of the solutions|
|Radiation||Scattering type: x-ray|
|Radiation wavelength||Relative weight: 1|
*PLUSHighest resolution: 2.25 Å / Rmerge(I) obs: 0.064
|Software||Name: PROFFT / Classification: refinement|
|Refinement||Resolution: 2.25→6 Å / |
|Refinement step||Cycle: LAST / Resolution: 2.25→6 Å|
|Refine LS restraints|
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