+Open data
-Basic information
Entry | Database: PDB / ID: 3qx5 | ||||||
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Title | Thrombin Inhibition by Pyridin Derivatives | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Serine Protease / Kringle / Hydrolase / Blood Coagulation / Blood Clotting / Convertion of Fibrinogen to Fibrin / Cleavage on Pairs of Basic Residues / Blood Clotting Inhibitor / Thrombin Inhibitor / Glycosylation / Blood / 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 / 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 / serine-type endopeptidase inhibitor activity / 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) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Biela, A. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin Authors: Biela, A. / Khayat, M. / Tan, H. / Kong, J. / Heine, A. / Hangauer, D. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qx5.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qx5.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qx5_validation.pdf.gz | 824 KB | Display | wwPDB validaton report |
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Full document | 3qx5_full_validation.pdf.gz | 826.5 KB | Display | |
Data in XML | 3qx5_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 3qx5_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/3qx5 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/3qx5 | HTTPS FTP |
-Related structure data
Related structure data | 3p17C 3qtoC 3qtvC 3qwcC 3shaC 3shcC 3si3C 3si4C 3sv2C 1h8dS C: citing same article (ref.) 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
-Protein/peptide , 2 types, 2 molecules LI
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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#3: Protein/peptide | Mass: 1662.683 Da / Num. of mol.: 1 / Fragment: residues in UNP 60-72 / Source method: obtained synthetically Details: Synthetic Fragment of Hirudin From Hirudo Medicinalis Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945 |
-Protein / Sugars , 2 types, 2 molecules H
#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 455 molecules
#5: Chemical | #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-GOL / | #8: Chemical | ChemComp-02P / | #9: 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: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 21, 2009 / Details: Collimating mirrors |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. all: 74225 / Num. obs: 74225 / % possible obs: 96 % / Redundancy: 3 % / Biso Wilson estimate: 10.94 Å2 / Rsym value: 0.048 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2719 / Rsym value: 0.293 / % possible all: 71.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H8D Resolution: 1.35→24.758 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.9298 / SU ML: 0.13 / Cross valid method: Free R / Phase error: 13.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.106 Å2 / ksol: 0.412 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.57 Å2 / Biso mean: 19.4443 Å2 / Biso min: 5.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→24.758 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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