+Open data
-Basic information
Entry | Database: PDB / ID: 2zfr | ||||||
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Title | Exploring thrombin S3 pocket | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Blood clotting/Hydrolase inhibitors / Acute phase / Cleavage on pair of basic residues / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Kringle / Protease / Secreted / Serine protease / Zymogen / Protease inhibitor / Serine protease inhibitor / Sulfation / 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 / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / 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 / FOURIER SYNTHESIS / Resolution: 1.85 Å | ||||||
Authors | Brandt, T. / Baum, B. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: Exploring thrombin S3 pocket Authors: Brandt, T. / Baum, B. / Hangauer, D. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zfr.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zfr.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zfr_validation.pdf.gz | 759.2 KB | Display | wwPDB validaton report |
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Full document | 2zfr_full_validation.pdf.gz | 765.5 KB | Display | |
Data in XML | 2zfr_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 2zfr_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/2zfr ftp://data.pdbj.org/pub/pdb/validation_reports/zf/2zfr | HTTPS FTP |
-Related structure data
Related structure data | 2zfqC 2zg0C 2zheC 2zhfC 2zhwC 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) / Tissue: Plasma / References: UniProt: P00734, thrombin |
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#3: Protein/peptide | Mass: 1534.554 Da / Num. of mol.: 1 / Fragment: Residues 53-64 / Source method: obtained synthetically Details: Synthetic fragment of hirudin from Hirudo Medicinalis Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945 |
-Protein , 1 types, 1 molecules H
#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 |
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-Non-polymers , 4 types, 163 molecules
#4: Chemical | #5: Chemical | ChemComp-46U / ( | #6: Chemical | ChemComp-GOL / | #7: 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: 2.52 Å3/Da / Density % sol: 51.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Phosphate buffer, sodium chloride, PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2007 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. all: 28636 / Num. obs: 28636 / % possible obs: 95.2 % / Redundancy: 2.7 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.055 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1427 / Rsym value: 0.356 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1H8D Resolution: 1.85→10 Å / Num. parameters: 10283 / Num. restraintsaints: 10113 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 2275 / Occupancy sum non hydrogen: 2515.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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