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Yorodumi- PDB-2hwl: Crystal structure of thrombin in complex with fibrinogen gamma' p... -
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-Basic information
Entry | Database: PDB / ID: 2hwl | ||||||
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Title | Crystal structure of thrombin in complex with fibrinogen gamma' peptide | ||||||
Components |
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Keywords | HYDROLASE / thrombin / fibrinogen / gamma' peptide / serine protease structure / allostery | ||||||
Function / homology | Function and homology information platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane ...platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to interleukin-6 / 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 / negative regulation of astrocyte differentiation / protein secretion / protein polymerization / cellular response to interleukin-1 / 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 / positive regulation of vasoconstriction / regulation of cytosolic calcium ion concentration / cell adhesion molecule binding / 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 / 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 / response to calcium ion / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / Signaling by BRAF and RAF1 fusions / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / Platelet degranulation / heparin binding / regulation of cell shape / ER-Phagosome pathway / positive regulation of cell growth / protein-containing complex assembly / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of ERK1 and ERK2 cascade / 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 / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Pineda, A.O. / Chen, Z.W. / Marino, F. / Mathews, F.S. / Mosesson, M.W. / Di Cera, E. | ||||||
Citation | Journal: Biophys.Chem. / Year: 2007 Title: Crystal structure of thrombin in complex with fibrinogen gamma' peptide. Authors: Pineda, A.O. / Chen, Z.W. / Marino, F. / Mathews, F.S. / Mosesson, M.W. / Di Cera, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hwl.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hwl.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/2hwl ftp://data.pdbj.org/pub/pdb/validation_reports/hw/2hwl | HTTPS FTP |
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-Related structure data
Related structure data | 1shhS 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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Details | The biological unit is a monomer composed of light and heavy chains. The structure has 2 molecules in the asymmetric unit, with a P21 spacegroup. |
-Components
-Protein/peptide , 2 types, 3 molecules ACP
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 2 / Fragment: Thrombin light chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: HPC4-pNUT / Organ (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin #3: Protein/peptide | | Mass: 1803.572 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The protein was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: P02679 |
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-Protein / Sugars , 2 types, 3 molecules BD
#2: Protein | Mass: 29694.102 Da / Num. of mol.: 2 / Fragment: Thrombin heavy chain / Mutation: R77AA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: HPC4-pNUT / Organ (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin #5: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 135 molecules
#4: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 4000, 100 mM HEPES sodium salt buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 148 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 27503 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.1 Å2 |
Reflection shell | Resolution: 2.4→2.55 Å / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1SHH Resolution: 2.4→40 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 346582.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.2479 Å2 / ksol: 0.344542 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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