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Yorodumi- PDB-1doj: Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1doj | ||||||
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Title | Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / thrombin / serine protease / enzyme inhibition / 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 / 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 / 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) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Recacha, R. / Costanzo, M.J. / Maryanoff, B.E. / Carson, M. / DeLucas, L. / Chattopadhyay, D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structure of human alpha-thrombin complexed with RWJ-51438 at 1.7 A: unusual perturbation of the 60A-60I insertion loop. Authors: Recacha, R. / Costanzo, M.J. / Maryanoff, B.E. / Carson, M. / DeLucas, L. / Chattopadhyay, D. #1: Journal: Biochemistry / Year: 1992 Title: Structure of the Hirulog 3-Thrombin Complex and Nature of the S' Subsites of Substrates and Inhibitors Authors: Qiu, X. / Padmanabhan, K.P. / Carperos, V.E. / Tulinsky, A. / Kline, T. / Maraganore, J.M. / Fenton II, J.W. #2: Journal: Biophys.J. / Year: 1996 Title: Crystal Structure of Thrombin with Thiazole-Containing Inhibitors: Probes of the S1' Binding Site Authors: Matthews, J.H. / Krishnan, R. / Costanzo, M.J. / Maryanoff, B.E. / Tulinsky, A. #3: Journal: Protein Sci. / Year: 1992 Title: The Refined 1.9-A X-ray Crystal Structure of D-Pro-Phe-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active- ...Title: The Refined 1.9-A X-ray Crystal Structure of D-Pro-Phe-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships Authors: Bode, W. / Turk, D. / Karshikov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1doj.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1doj.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 1doj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/1doj ftp://data.pdbj.org/pub/pdb/validation_reports/do/1doj | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
-Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB
#1: Protein | Mass: 33858.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cellular location: PLASMA / References: UniProt: P00734, thrombin |
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#2: Protein/peptide | Mass: 1491.528 Da / Num. of mol.: 1 / Fragment: FRAGMENT OF HIRUDIN / Source method: obtained synthetically / Details: Hirugen, comes from hirudin / References: UniProt: P09945, UniProt: P28504*PLUS |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 352 molecules
#3: Chemical | ChemComp-1Z0 / | ||
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#5: Chemical | #6: 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: 2.47 Å3/Da / Density % sol: 50.21 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.75 sodium acetate, 0.01% (w/v), 20% polyethylene glycol 4000 (w/v), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.3 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 4, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→99 Å / Num. all: 126549 / Num. obs: 126549 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.3 |
Reflection shell | Highest resolution: 1.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2 / % possible all: 87.1 |
Reflection | *PLUS Num. obs: 42979 / Num. measured all: 289770 |
Reflection shell | *PLUS Lowest resolution: 1.72 Å / % possible obs: 43 % / Rmerge(I) obs: 0.2 |
-Processing
Software |
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Refinement | Resolution: 1.7→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1520225.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 0 / Details: The Bijvoet differences were used in phasing
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 93.48 Å2 / ksol: 0.49 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 35906 / σ(F): 3 / % reflection Rfree: 4.5 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.232 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.298 / % reflection Rfree: 10 % / Rfactor Rwork: 0.276 |