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Yorodumi- PDB-1eb1: Complex structure of human thrombin with N-methyl-arginine inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eb1 | ||||||
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Title | Complex structure of human thrombin with N-methyl-arginine inhibitor | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / BLOOD COAGULATION / CALCIUM-BINDING / GLYCOPROTEIN / KRINGLE / HYDROLASE-HYDROLASE 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 / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / 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 / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / Regulation of Complement cascade / acute-phase response / 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 / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / 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) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / 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 / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Friedrich, R. / Steinmetzer, T. / Bode, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The Methyl Group of N(Alpha)(Me)Arg-Containing Peptides Disturbs the Active-Site Geometry of Thrombin, Impairing Efficient Cleavage Authors: Friedrich, R. / Steinmetzer, T. / Huber, R. / Sturzebecher, J. / Bode, W. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eb1.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eb1.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 1eb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/1eb1 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/1eb1 | HTTPS FTP |
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-Related structure data
Related structure data | 2hgtS 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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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 1209.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#2: Protein | Mass: 29594.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: BLOOD / References: UniProt: P00734 |
#3: Protein/peptide | Mass: 3188.627 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN RESIDUES 364-620 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: BLOOD / References: UniProt: P00734, thrombin |
#4: Protein/peptide | |
#5: Water | ChemComp-HOH / |
Sequence details | BASED ON THE PRIMARY PUBLICATION J MOL BIOL. 2002 MAR 1;316(4):869- 74, THE LIGAND E1A WAS THE N- ...BASED ON THE PRIMARY PUBLICATIO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | pH: 8 / Details: PH 8.00 |
Crystal grow | *PLUS Method: other / Details: Steinmetzer, T., (2000) Biol. Chem., 381, 603. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→17 Å / Num. obs: 30387 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.5 / % possible all: 92.6 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 17 Å / Redundancy: 2.2 % / Num. measured all: 156090 |
Reflection shell | *PLUS % possible obs: 92.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HGT Resolution: 1.8→16.74 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1230607.77 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→16.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 17 Å / Num. reflection obs: 29169 / Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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