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Yorodumi- PDB-1d3t: CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B... -
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Entry | Database: PDB / ID: 1d3t | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 1 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / THROMBIN / BENZO[B]THIOPHENE / BLOOD CLOTTING / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of serine-type peptidase activity / 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 ...negative regulation of serine-type peptidase activity / 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 / 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 / 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 / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / 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) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Chirgadze, N.Y. | ||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: The crystal structures of human alpha-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives: a binding mode for a structurally novel class of inhibitors. Authors: Chirgadze, N.Y. / Sall, D.J. / Briggs, S.L. / Clawson, D.K. / Zhang, M. / Smith, G.F. / Schevitz, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 1d3t.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d3t.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d3t_validation.pdf.gz | 482.5 KB | Display | wwPDB validaton report |
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Full document | 1d3t_full_validation.pdf.gz | 494.9 KB | Display | |
Data in XML | 1d3t_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 1d3t_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/1d3t ftp://data.pdbj.org/pub/pdb/validation_reports/d3/1d3t | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein/peptide , 2 types, 2 molecules AH
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P00734, thrombin |
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#3: Protein/peptide | Mass: 1548.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hirudo medicinalis (medicinal leech) / References: UniProt: P28501, UniProt: P01050*PLUS |
-Protein / Sugars , 2 types, 2 molecules B
#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P00734, thrombin |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 3 molecules
#5: Chemical | #6: Chemical | ChemComp-BT1 / { | |
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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: 2.8 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 30% PEG 3400; 100 mM sodium citrate; 200 mM ammonium acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: YALE/MSC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 5736 / % possible obs: 79.7 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3.1 / % possible all: 81 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 0 / Num. measured all: 24280 |
Reflection shell | *PLUS % possible obs: 81.1 % |
-Processing
Software |
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Refinement | Resolution: 3→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.14 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 98 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.398 / % reflection Rfree: 6.7 % / Rfactor Rwork: 0.297 |