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- PDB-1oyt: COMPLEX OF RECOMBINANT HUMAN THROMBIN WITH A DESIGNED FLUORINATED... -
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Basic information
Entry | Database: PDB / ID: 1oyt | ||||||
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Title | COMPLEX OF RECOMBINANT HUMAN THROMBIN WITH A DESIGNED FLUORINATED INHIBITOR | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() 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 / fibrinolysis / regulation of cytosolic calcium ion concentration / 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 / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Banner, D.W. / Olsen, J.A. | ||||||
![]() | ![]() Title: A Fluorine Scan of Thrombin Inhibitors to Map the Fluorophilicity/Fluorophobicity of an Enzyme Active Site: Evidence for CF...C=O Interactions. Authors: Olsen, J.A. / Banner, D.W. / Seiler, P. / Obst-Sander, U. / D'Arcy, A. / Stihle, M. / Mueller, K. / Diederich, F. #1: ![]() Title: Stable expression and purification of a secreted human recombinant prethrombin-2 and its activation to thrombin Authors: Russo, G. / Gast, A. / Schlaeger, E.J. / Angiolillo, A. / Pietropaolo, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.7 KB | Display | ![]() |
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PDB format | ![]() | 62 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.6 KB | Display | ![]() |
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Full document | ![]() | 780.3 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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
-Protein , 1 types, 1 molecules H
#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 407 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/FSN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/FSN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NA / |
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#5: Chemical | ChemComp-CA / |
#6: Chemical | ChemComp-FSN / ( |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % | ||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.4 / Method: unknown | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 24, 2002 / Details: Osmic mirrors |
Radiation | Monochromator: OSMICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→20 Å / Num. all: 44106 / Num. obs: 38758 / % possible obs: 87.9 % / Observed criterion σ(I): -3 / Redundancy: 7.33 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.042 / Net I/σ(I): 33.43 |
Reflection shell | Resolution: 1.64→1.74 Å / Redundancy: 6.25 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 9.71 / Num. unique all: 7048 / Rsym value: 0.17 / % possible all: 53 |
Reflection | *PLUS Highest resolution: 1.67 Å / Num. measured all: 284109 / Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 9.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: IN HOUSE THROMBIN STRUCTURES Resolution: 1.67→19.3 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J. 8, 3467-3475). Double ...Details: CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J. 8, 3467-3475). Double confromations given as single conformer are: H chain Leu41, Arg50, Leu64, Val66, Leu85, Met106, Ser129B Leu130, Asp186. Gly186C has a second trace with psi of 186D + 180degrees. Missing residues H chain: 148 loop WTANVGK, residues Thr147 and Gln151 weak. Missing residues L chain: N-terminus TFGSGE, C-terminus DGR. Missing from 'hirugen' I chain: C-terminus EEYLQ. Hirugen corresponds to hirudin 55-65, is synthesized chemically, is not sulphated. Asp 55 has no amino group and thus is given as a succinic acid residue. Arg75 has 2 conformations. COORDINATES ARE GIVEN UP TO CB. WATERS 107 AND 35 INDICATE THE GUANIDINIUM POSITION ON THE 2-FOLD AXIS. Residues with some or all atoms at 0.5 occupancy are L chain: Asp1A, Lys14A, Arg14D, Ile14K, H chain: Leu41, Lys81, Lys110, Pro111, Arg126, Glu127, Ser129B, Thr147, Gln151, Asp186A, Lys186D, Glu192, Asn205, Lys236 Gln239, Lys240, Gln244, I chain Glu4, Pro6. Atoms with zero occupancy H chain Ser36A Og and Asn62 OD1. The sugar on Asn62 is not modelled (water molecules). All inhibitor atoms refine to B-values < 25. The weakest is O18. Between O18 and the NZ of K60F is a smear of density, not well fitted by water 233.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.7734 Å2 / ksol: 0.312145 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2
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Refine analyze | Luzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.12 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→19.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.73 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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Refine LS restraints | *PLUS
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