+Open data
-Basic information
Entry | Database: PDB / ID: 1bcu | ||||||
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Title | ALPHA-THROMBIN COMPLEXED WITH HIRUGEN AND PROFLAVIN | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / COMPLEX (SERINE PROTEASE INHIBITOR) / HYDROLASE / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of serine-type peptidase activity / positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / 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 / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / 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 / positive regulation of receptor signaling pathway via JAK-STAT / lipopolysaccharide binding / 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 / 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 / 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 / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Hirudo medicinalis (medicinal leech) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Conti, E. / Rivetti, C. / Wonacott, A. / Brick, P. | ||||||
Citation | Journal: FEBS Lett. / Year: 1998 Title: X-ray and spectrophotometric studies of the binding of proflavin to the S1 specificity pocket of human alpha-thrombin. Authors: Conti, E. / Rivetti, C. / Wonacott, A. / Brick, P. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin Authors: Skrzypczak-Jankun, E. / Carperos, V.E. / Ravichandran, K.G. / Tulinsky, A. / Westbrook, M. / Maraganore, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bcu.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bcu.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 1bcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bcu_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 1bcu_full_validation.pdf.gz | 445 KB | Display | |
Data in XML | 1bcu_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1bcu_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/1bcu ftp://data.pdbj.org/pub/pdb/validation_reports/bc/1bcu | HTTPS FTP |
-Related structure data
Related structure data | 1hgtS 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: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P00734, thrombin |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P00734, thrombin |
#3: Protein/peptide | Mass: 1548.580 Da / Num. of mol.: 1 / Fragment: RESIDUES 54-65 OF HIRUDIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / References: UniProt: P01050 |
#4: Chemical | ChemComp-PRL / |
#5: Water | ChemComp-HOH / |
Compound details | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *I* IS USED FOR HIRUGEN. THE HIRUGEN RESIDUE NUMBERING CORRESPOND |
Sequence details | CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT ...CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.51 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1994 / Details: PINHOLE |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 56491 / % possible obs: 98.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.158 / % possible all: 95.9 |
Reflection | *PLUS Num. obs: 24042 / Num. measured all: 56491 |
Reflection shell | *PLUS % possible obs: 94.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HGT Resolution: 2→20 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT Details: THE SIDE CHAIN OF ARG H 75 HAS BEEN MODELED WITH TWO DIFFERENT CONFORMATIONS.
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Displacement parameters | Biso mean: 29.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.31 / Rfactor Rwork: 0.29 |