+Open data
-Basic information
Entry | Database: PDB / ID: 2cf8 | ||||||
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Title | Complex of recombinant human thrombin with an inhibitor | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE/INHIBITOR / ACUTE PHASE / BLOOD COAGULATION / CALCIUM-BINDING / GLYCOPROTEIN / HYDOLASE / SERINE PROTEASE / SERINE PROTEASE INHIBITOR COMPLEX / COMPLEX HYDROLASE-INHIBITOR / 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / 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 / Regulation of Complement cascade / acute-phase response / lipopolysaccharide binding / Cell surface interactions at the vascular wall / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / response to wounding / platelet activation / Golgi lumen / positive regulation of protein localization to nucleus / 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 / G alpha (q) signalling events / positive regulation of cell growth / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / 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: 1.3 Å | ||||||
Authors | Schweizer, E. / Hoffmann-Roeder, A. / Olsen, J.A. / Obst-Sander, U. / Wagner, B. / Kansy, M. / Banner, D.W. / Diederich, F. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2006 Title: Multipolar Interactions in the D Pocket of Thrombin: Large Differences between Tricyclic Imide and Lactam Inhibitors. Authors: Schweizer, E. / Hoffmann-Roeder, A. / Olsen, J.A. / Seiler, P. / Obst-Sander, U. / Wagner, B. / Kansy, M. / Banner, D.W. / Diederich, F. | ||||||
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 A 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 | 2cf8.cif.gz | 133.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cf8.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 2cf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/2cf8 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/2cf8 | HTTPS FTP |
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-Related structure data
Related structure data | 2cf9C 1oytS 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 , 1 types, 1 molecules H
#1: Protein | Mass: 29594.055 Da / Num. of mol.: 1 / Fragment: CATALYTIC, RESIDUES 364-620 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P00734, thrombin |
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-Protein/peptide , 2 types, 2 molecules IL
#2: Protein/peptide | |
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#3: Protein/peptide | Mass: 3303.715 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 334-361 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P00734, thrombin |
-Non-polymers , 4 types, 400 molecules
#4: Chemical | ChemComp-ESH / |
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#5: Chemical | ChemComp-NA / |
#6: Chemical | ChemComp-CA / |
#7: 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: 2.76 Å3/Da / Density % sol: 43 % |
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Crystal grow | pH: 7.4 / Details: PH 7.40 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97001 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 28, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97001 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→20 Å / Num. obs: 85919 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.58 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 3.08 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.2 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1OYT Resolution: 1.3→71.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.577 / SU ML: 0.034 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE CHAIN OF ARG 75 HAS ALTERNATIVE CONFORMATIONS, ONE OF WHICH IS ON A DIAD AXIS. IT HAS NOT BEEN MODELLED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→71.25 Å
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Refine LS restraints |
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