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Yorodumi- PDB-4udw: Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4udw | |||||||||
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Title | Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2, 5dichlorophenyl)methylpyrrolidine-2-carboxamide | |||||||||
Components |
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Keywords | HYDROLASE / HYDROLASE INHIBITOR COMPLEX / SERINE PROTEASE / BLOOD COAGULATION / BLOOD CLOTTING / CONVERTION OF FIBRINOGEN TO FIBRIN / BLOOD CLOTTING INHIBITOR / THROMBIN INHIBITOR / FRAGMENT / GLYCOSYLATION / BLOOD | |||||||||
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: 1.16 Å | |||||||||
Authors | Ruehmann, E. / Heine, A. / Klebe, G. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why. Authors: Ruehmann, E. / Betz, M. / Heine, A. / Klebe, G. | |||||||||
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 | 4udw.cif.gz | 205.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4udw.ent.gz | 165.9 KB | Display | PDB format |
PDBx/mmJSON format | 4udw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4udw_validation.pdf.gz | 824.9 KB | Display | wwPDB validaton report |
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Full document | 4udw_full_validation.pdf.gz | 825.5 KB | Display | |
Data in XML | 4udw_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 4udw_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/4udw ftp://data.pdbj.org/pub/pdb/validation_reports/ud/4udw | HTTPS FTP |
-Related structure data
Related structure data | 4ud9C 4ue7C 4uehC 5af9C 5afyC 5afzC 5ahgC 1h8dS 4udh 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 IL
#2: Protein/peptide | Mass: 1491.528 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 62-72 / Source method: obtained synthetically / Details: HIRUDIN (54-65) (SULFATED) / Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P09945 |
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#3: Protein/peptide | Mass: 3317.741 Da / Num. of mol.: 1 / Fragment: THROMBIN LIGHT CHAIN, UNP RESIDUES 333-360 / Source method: isolated from a natural source / Details: PURIFIED FROM HUMAN BLOOD PLASMA / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00734, thrombin |
-Protein / Sugars , 2 types, 2 molecules H
#1: Protein | Mass: 29651.105 Da / Num. of mol.: 1 / Fragment: THROMBIN HEAVY CHAIN, UNP RESIDUES 364-620 / Source method: isolated from a natural source / Details: PURIFIED FROM HUMAN BLOOD PLASMA / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00734, thrombin |
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#8: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 314 molecules
#4: Chemical | #5: Chemical | ChemComp-N6L / | #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | ASP 14L WAS NOT BUILD DUE TO LACK OF ELECTRON DESITY RESIDUES 148-149E WERE NOT BUILD DUE TO LACK ...ASP 14L WAS NOT BUILD DUE TO LACK OF ELECTRON DESITY RESIDUES 148-149E WERE NOT BUILD DUE TO LACK OF ELECTRON DESITY GLY 554 WAS NOT BUILD DUE TO LACK OF ELECTRON DESITY |
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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: 2.45 Å3/Da / Density % sol: 49.7 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→71.13 Å / Num. obs: 116096 / % possible obs: 97 % / Observed criterion σ(I): 2.7 / Redundancy: 4.4 % / Biso Wilson estimate: 13.15 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 25.92 |
Reflection shell | Resolution: 1.16→1.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H8D Resolution: 1.16→71.131 Å / SU ML: 0.08 / σ(F): 1.35 / Phase error: 13.07 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE NOT MODELED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→71.131 Å
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Refine LS restraints |
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LS refinement shell |
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