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Yorodumi- PDB-1dm4: SER195ALA MUTANT OF HUMAN THROMBIN COMPLEXED WITH FIBRINOPEPTIDE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dm4 | ||||||
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Title | SER195ALA MUTANT OF HUMAN THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A (7-16) | ||||||
Components |
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Keywords | HYDROLASE / MUTANT THROMBIN / RESIDUAL CATALYTIC ACTIVITY / FIBRINOPEPTIDE A | ||||||
Function / homology | Function and homology information blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / platelet alpha granule / 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 / blood coagulation, fibrin clot formation / platelet alpha granule / 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 / neutrophil-mediated killing of gram-negative bacterium / positive regulation of peptide hormone secretion / positive regulation of exocytosis / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of platelet activation / negative regulation of astrocyte differentiation / protein polymerization / 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 / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / Integrin signaling / cell-matrix adhesion / 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 / positive regulation of protein secretion / 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 / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of insulin secretion / platelet aggregation / platelet activation / response to wounding / Golgi lumen / response to calcium ion / 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) / Signaling by RAF1 mutants / extracellular vesicle / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / positive regulation of reactive oxygen species metabolic process / Signaling by BRAF and RAF1 fusions / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / Platelet degranulation / heparin binding / ER-Phagosome pathway / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / protein-containing complex assembly / collagen-containing extracellular matrix / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Krishnan, R. / Sadler, E.J. / Tulinsky, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structure of the Ser195Ala mutant of human alpha--thrombin complexed with fibrinopeptide A(7--16): evidence for residual catalytic activity. Authors: Krishnan, R. / Sadler, J.E. / Tulinsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dm4.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dm4.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dm4 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dm4 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3939.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00734 |
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#2: Protein | Mass: 29921.414 Da / Num. of mol.: 1 / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00734 |
#3: Protein/peptide | Mass: 1047.144 Da / Num. of mol.: 1 / Fragment: FPA / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / References: UniProt: P02671*PLUS |
#4: 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: 2.94 Å3/Da / Density % sol: 58.19 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 1.4M SODIUM CITRATE, 1-2% ISOPROPANOL, 0.1M HEPES BUFFER, pH 7.50 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 7, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. obs: 9561 / % possible obs: 71 % / Observed criterion σ(I): 2 / Redundancy: 2.28 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.5→2.75 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.19 / % possible all: 94.6 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 15 Å / Observed criterion σ(I): 2 / Num. measured all: 21833 |
Reflection shell | *PLUS % possible obs: 61 % |
-Processing
Software |
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Refinement | Resolution: 2.5→7 Å / σ(F): 4 / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE. /
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Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.169 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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