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- PDB-1ppb: THE REFINED 1.9 ANGSTROMS CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMB... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ppb | ||||||
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Title | THE REFINED 1.9 ANGSTROMS CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN: INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE AND SIGNIFICANCE OF THE TYR-PRO-PRO-TRP INSERTION SEGMENT | ||||||
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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 / 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 | ![]() | ||||||
![]() | Bode, W. | ||||||
![]() | ![]() Title: The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment. Authors: Bode, W. / Mayr, I. / Baumann, U. / Huber, R. / Stone, S.R. / Hofsteenge, J. #1: ![]() Title: The Refined 1.9-Angstroms Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin. Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active- ...Title: The Refined 1.9-Angstroms Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin. Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Properties Authors: Bode, W. / Turk, D. / Karshikov, A. #2: ![]() Title: Electrostatic Interactions in the Association of Proteins: An Analysis of the Thrombin-Hirudin Complex Authors: Karshikov, A. / Bode, W. / Tulinsky, A. / Stone, S.R. #3: ![]() Title: Refined 2.3 Angstroms X-Ray Crystal Structure of Bovine Thrombin Complexes Formed with the Benzamidine and Arginine-Based Thrombin Inhibitors Napap, 4-Tapap and Mqpa. A Starting Point for ...Title: Refined 2.3 Angstroms X-Ray Crystal Structure of Bovine Thrombin Complexes Formed with the Benzamidine and Arginine-Based Thrombin Inhibitors Napap, 4-Tapap and Mqpa. A Starting Point for Improving Anti-Thrombotics Authors: Brandstetter, H. / Turk, D. / Hoeffken, H.W. / Grosse, D. / Stuerzebecher, J. / Martin, P.D. / Edwards, B.F.P. / Bode, W. #4: ![]() Title: The Interaction of Thrombin with Fibrinogen. A Structural Basis for its Specificity Authors: Stubbs, M.T. / Oschkinat, H. / Mayr, I. / Huber, R. / Angliker, H. / Stone, S.R. / Bode, W. #5: ![]() Title: X-Ray Crystal Structures of Human Alpha-Thrombin and of the Human Thrombin-Hirudin Complex Authors: Bode, W. / Huber, R. / Rydel, T.J. / Tulinsky, A. #6: ![]() Title: The Spatial Structure of Thrombin as a Guide to its Multiple Sites of Interaction Authors: Bode, W. / Stubbs, M. #7: ![]() Title: The Electrostatic Properties of Thrombin: Importance for Structural Stabilization and Ligand Binding Authors: Karshikov, A. / Bode, W. #8: ![]() Title: Refined Structure of the Hirudin-Thrombin Complex Authors: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R. #9: ![]() Title: Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophe Authors: Bode, W. / Turk, D. / Stuerzebecher, J. #10: ![]() Title: The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin Authors: Rydel, T.J. / Ravichandran, K.G. / Tulinsky, A. / Bode, W. / Huber, R. / Roitsch, C. / Fenton II, J.W. #11: ![]() Title: Crystal Structure of the Thrombin-Hirudin Complex: A Novel Mode of Serine Protease Inhibition Authors: Gruetter, M.G. / Priestle, J.P. / Rahnel, J. / Grossenbacher, H. / Bode, W. / Hofsteenge, J. / Stone, S.R. #12: ![]() Title: Human D-Phe-Pro-Arg-Ch2-Alpha-Thrombin Crystallization and Diffraction Data Authors: Skrzypczak-Jankun, E. / Rydel, T.J. / Tulinsky, A. / Fenton II, J.W. / Mann, K.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.2 KB | Display | ![]() |
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PDB format | ![]() | 63.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.3 KB | Display | ![]() |
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Full document | ![]() | 471 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 15.8 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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1 |
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Unit cell |
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Atom site foot note | 1: THR L 1H - PHE L 1G OMEGA ANGLE = 227.924 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: TYR L 14J - ILE L 14K OMEGA ANGLE = 121.634 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: ILE L 14K - ASP L 14L OMEGA ANGLE = 127.868 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: GLY L 14M - ARG L 15 OMEGA ANGLE = 225.554 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: CIS PROLINE - PRO H 37A 6: SER H 129B - LEU H 129C OMEGA ANGLE = 217.470 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 7: PHE H 204A - ASN H 204B OMEGA ANGLE = 137.433 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 8: GLU H 217 - GLY H 219 OMEGA ANGLE = 210.043 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 9: PHE I 1 IS A D-AMINO ACID. |
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Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
#3: Chemical | ChemComp-0G6 / |
#4: Water | ChemComp-HOH / |
Compound details | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN |
Nonpolymer details | D-PHE-PRO-ARG-CHLOROMETHYLKETONE HAS FORMED TWO COVALENT CONNECTIONS TO THROMBIN: 1) VIA A ...D-PHE-PRO-ARG-CHLOROMETH |
Sequence details | CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT ...CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.54 % | |||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: microdialysis | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 16910 / Rmerge(I) obs: 0.121 |
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Processing
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Refinement | Rfactor Rwork: 0.156 / Rfactor obs: 0.156 / Highest resolution: 1.92 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.92 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.92 Å / Rfactor obs: 0.156 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.137 |