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Yorodumi- PDB-1fph: THE INTERACTION OF THROMBIN WITH FIBRINOGEN: A STRUCTURAL BASIS F... -
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-Basic information
Entry | Database: PDB / ID: 1fph | ||||||
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Title | THE INTERACTION OF THROMBIN WITH FIBRINOGEN: A STRUCTURAL BASIS FOR ITS SPECIFICITY | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / 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 / positive regulation of peptide hormone secretion / regulation of blood coagulation / positive regulation of exocytosis / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of vasoconstriction / negative regulation of astrocyte differentiation / protein polymerization / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / Integrin cell surface interactions / 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 / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / Peptide ligand-binding receptors / cell-matrix adhesion / positive regulation of release of sequestered calcium ion into cytosol / platelet alpha granule lumen / acute-phase response / Regulation of Complement cascade / positive regulation of protein secretion / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / Post-translational protein phosphorylation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / Signaling by high-kinase activity BRAF mutants / response to calcium ion / MAP2K and MAPK activation / positive regulation of insulin secretion / platelet activation / platelet aggregation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / 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 / serine-type endopeptidase inhibitor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / Signaling by BRAF and RAF1 fusions / blood coagulation / extracellular vesicle / Thrombin signalling through proteinase activated receptors (PARs) / Platelet degranulation / heparin binding / positive regulation of cell growth / protein-macromolecule adaptor activity / regulation of cell shape / ER-Phagosome pathway / protein-containing complex assembly / G alpha (q) signalling events / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Stubbs, M.T. / Bode, W. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1992 Title: The interaction of thrombin with fibrinogen. A structural basis for its specificity. Authors: Stubbs, M.T. / Oschkinat, H. / Mayr, I. / Huber, R. / Angliker, H. / Stone, S.R. / Bode, W. #1: Journal: Thromb.Res. / Year: 1993 Title: A Player of Many Parts: The Spotlight Falls on Thrombin'S Structure Authors: Stubbs, M.T. / Bode, W. #2: Journal: Protein Sci. / Year: 1992 Title: The Refined 1.9 Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed ...Title: The Refined 1.9 Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships Authors: Bode, W. / Turk, D. / Karshikov, A. #3: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Structure of the Hirudin-Thrombin Complex Authors: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fph.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fph.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fph_validation.pdf.gz | 391.5 KB | Display | wwPDB validaton report |
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Full document | 1fph_full_validation.pdf.gz | 400.6 KB | Display | |
Data in XML | 1fph_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 1fph_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/1fph ftp://data.pdbj.org/pub/pdb/validation_reports/fp/1fph | 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
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
#3: Protein/peptide | Mass: 1468.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (natural) Hirudo medicinalis (medicinal leech) / References: UniProt: P28506*PLUS |
#4: Protein/peptide | |
#5: Water | ChemComp-HOH / |
Compound details | THE FIBRINOPEPTIDE A CONTAINS A C-TERMINAL CHLOROMETHYLKETONE GROUP TO FORM COVALENT BONDS WITH THE ...THE FIBRINOPEP |
Sequence details | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *I* IS USED FOR HIRUDIN. CHAIN INDICATOR *F* IS USED FOR FIBRINOPEP |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.83 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 11767 / % possible obs: 61 % / Num. measured all: 40715 / Rmerge(I) obs: 0.105 |
-Processing
Software | Name: EREF / Classification: refinement | ||||||||||||
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Refinement | Rfactor Rwork: 0.166 / Highest resolution: 2.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refinement | *PLUS Highest resolution: 2.5 Å / Rfactor obs: 0.166 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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