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Yorodumi- PDB-5jfd: Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jfd | ||||||
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Title | Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-D-arginyl)pyrrolidine-2-carboxamide | ||||||
Components |
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Keywords | HYDROLASE / COAGULATION / BLOOD CLOTTING / CONVERTION OF FIBRINOGEN TO FIBRIN / BLOOD CLOTTING INHIBITOR / THROMBIN INHIBITOR / PREORGANIZATION / GLYCOSYLATION / BLOOD | ||||||
Function / homology | Function and homology information 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 ...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 | Homo sapiens (human) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Sandner, A. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. Authors: Sandner, A. / Hufner-Wulsdorf, T. / Heine, A. / Steinmetzer, T. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jfd.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jfd.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jfd_validation.pdf.gz | 884.3 KB | Display | wwPDB validaton report |
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Full document | 5jfd_full_validation.pdf.gz | 884.4 KB | Display | |
Data in XML | 5jfd_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 5jfd_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/5jfd ftp://data.pdbj.org/pub/pdb/validation_reports/jf/5jfd | HTTPS FTP |
-Related structure data
Related structure data | 5jzyC 5lceC 5lpdC 6gbwC 6rotC 1h8dS S: Starting model for refinement C: citing same article (ref.) |
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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) / Plasmid details: PURIFIED FROM HUMAN BLOOD PLASMA / Tissue: Blood / References: UniProt: P00734, thrombin |
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#3: Protein/peptide | Mass: 1548.580 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: http://shop.bachem.com/h-7425.html contains sulfated tyrosine 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) / Plasmid details: PURIFIED FROM HUMAN BLOOD PLASMA / Tissue: Blood / References: UniProt: P00734, thrombin |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 270 molecules
#4: Chemical | ChemComp-2TS / ( | ||||||
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#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-DMS / | #9: Water | ChemComp-HOH / | |
-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: 51.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 mM Sodium dihydrogen phosphate ph 7.5, 350 mM NACl, 27% PEG 8000, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2015 / Details: Sagitally bended Si111-crystal |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→43.13 Å / Num. obs: 58841 / % possible obs: 97.3 % / Redundancy: 2.8 % / CC1/2: 0.999 / Rsym value: 0.039 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.46→1.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H8D Resolution: 1.46→43.13 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.29 / Details: Phenix refinement
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→43.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.4823 Å
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