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Yorodumi- PDB-1de7: INTERACTION OF FACTOR XIII ACTIVATION PEPTIDE WITH ALPHA-THROMBIN... -
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-Basic information
Entry | Database: PDB / ID: 1de7 | ||||||
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Title | INTERACTION OF FACTOR XIII ACTIVATION PEPTIDE WITH ALPHA-THROMBIN: CRYSTAL STRUCTURE OF THE ENZYME-SUBSTRATE COMPLEX | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE SUBSTRATE / ENZYME-SUBSTRATE COMPLEX / ALPHA-THROMBIN / FACTOR XIII ACTIVATION PEPTIDE / HYDROLASE/PEPTIDE / BLOOD CLOTTING / HYDROLASE-HYDROLASE SUBSTRATE 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 / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / 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 / 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 / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / 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 / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / positive regulation of cell growth / regulation of cell shape / G alpha (q) signalling events / collagen-containing extracellular matrix / 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 / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sadasivan, C. / Yee, V.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Interaction of the factor XIII activation peptide with alpha -thrombin. Crystal structure of its enzyme-substrate analog complex. Authors: Sadasivan, C. / Yee, V.C. #1: 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. #2: 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. / Mayer, I. / Huber, R. / Angliker, H. / Stoner, S.R. / Bode, W. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Three-Dimensional Structure of a Transglutaminase: Human Blood Coagulation Factor Xiii Authors: Yee, V.C. / Pedersen, L.C. / Trong, I.L. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1de7.cif.gz | 141.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1de7.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 1de7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1de7_validation.pdf.gz | 461.3 KB | Display | wwPDB validaton report |
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Full document | 1de7_full_validation.pdf.gz | 469.2 KB | Display | |
Data in XML | 1de7_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 1de7_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/1de7 ftp://data.pdbj.org/pub/pdb/validation_reports/de/1de7 | HTTPS FTP |
-Related structure data
Related structure data | 1ahtS 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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2 |
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Unit cell |
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Details | THERE ARE TWO INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT: COMPLEX 1 ALPHA-THROMBIN: CHAINS L, H FACTOR XIII PEPTIDE: CHAIN A COMPLEX 2 ALPHA-THROMBIN: CHAINS J, K FACTOR XIII PEPTIDE: CHAIN B |
-Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P00734, thrombin #2: Protein | Mass: 29780.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P00734, thrombin #3: Protein/peptide | Mass: 1132.761 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | THE FACTOR XIII DERIVED PEPTIDE CONTAIN A C-TERMINAL CHLOROMETHYLKETONE GROUP AND IS COVALENTLY ...THE FACTOR XIII DERIVED PEPTIDE CONTAIN A C-TERMINAL CHLOROMETH | Sequence details | CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED FOR THROMBIN, BASED ON THE ...CHYMOTRYPS | |
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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: 2.7 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: PEG8000, SODIUM CHLORIDE, SODIUM CITRATE, pH 5.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 10, 1998 / Details: YALE MIRROR |
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→25 Å / Num. obs: 45245 / % possible obs: 91.8 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.157 / % possible all: 79.3 |
Reflection | *PLUS Num. measured all: 124210 |
Reflection shell | *PLUS % possible obs: 79.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: THROMBIN CRYSTAL STRUCTURE WITH PDB ID 1AHT Resolution: 2→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARAM19.PRO / Topol file: TOPH19.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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