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Yorodumi- PDB-1tmt: CHANGES IN INTERACTIONS IN COMPLEXES OF HIRUDIN DERIVATIVES AND H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tmt | ||||||
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Title | CHANGES IN INTERACTIONS IN COMPLEXES OF HIRUDIN DERIVATIVES AND HUMAN ALPHA-THROMBIN DUE TO DIFFERENT CRYSTAL FORMS | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / COMPLEX / SERINE PROTEASE / INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of serine-type peptidase activity / 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 ...negative regulation of serine-type peptidase activity / 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 / negative regulation of cytokine production involved in inflammatory response / positive regulation of collagen biosynthetic process / 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 / Cell surface interactions at the vascular wall / lipopolysaccharide binding / 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 / platelet activation / response to wounding / 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 / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / 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) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Priestle, J.P. / Gruetter, M.G. | ||||||
Citation | Journal: Protein Sci. / Year: 1993 Title: Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms. Authors: Priestle, J.P. / Rahuel, J. / Rink, H. / Tones, M. / Grutter, M.G. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Structure of the Hirugen and Hirulog Complexes of Alpha-Thrombin Authors: Skrzypczak-Jankun, E. / Carperos, V.E. / Ravichandran, K.G. / Tulinsky, A. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Structure of the Hirudin-Thrombin Complex Authors: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R. #3: Journal: Embo J. / Year: 1990 Title: Crystal Structure of the Thrombin-Hirudin Complex: A Novel Mode of Serine Protease Inhibition Authors: Gruetter, M.G. / Priestle, J.P. / Rahuel, J. / Grossenbacher, H. / Bode, W. / Hofsteenge, J. / Stone, S.R. #4: Journal: Embo J. / Year: 1989 Title: The Refined 1.9 Angstrom 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. | ||||||
History |
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Remark 700 | SHEET THE SHEET PRESENTED AS *BS1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *BS1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS *BS2* ON SHEET RECORDS BELOW IS ACTUALLY A SEVEN-STRANDED BETA- BARREL. THIS IS REPRESENTED BY AN EIGHT-STRANDED SHEET IN WHICH THE FIRST AND SECOND TO LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tmt.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tmt.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/1tmt ftp://data.pdbj.org/pub/pdb/validation_reports/tm/1tmt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO H 37 / 2: RESIDUE DPN I 1 OF INHIBITOR CGP 50,856 IS A D-PHE. 3: RESIDUE TYR J 63 OF INHIBITOR CGP 50,856 IS NOT SULFATED AS IT IS IN NATIVE HIRUDIN. |
-Components
-ALPHA-THROMBIN ... , 2 types, 2 molecules LH
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00734, thrombin |
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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.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00734, thrombin |
-CGP 50,856 INHIBITOR, cleaved ... , 2 types, 2 molecules IJ
#3: Protein/peptide | |
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#4: Protein/peptide | Mass: 1908.927 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: P28504 |
-Sugars / Non-polymers , 2 types, 112 molecules
#5: Sugar | ChemComp-NAG / |
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#6: Water | ChemComp-HOH / |
-Details
Compound details | RESIDUE DPN I 1 OF INHIBITOR CGP 50,856 IS A D-PHE. THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. ...RESIDUE DPN I 1 OF INHIBITOR CGP 50,856 IS A D-PHE. THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER |
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Nonpolymer details | RESIDUE TYR J 63 OF INHIBITOR CGP 50,856 IS NOT SULFATED AS IT IS IN NATIVE HIRUDIN. |
Sequence details | 1. CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ...1. CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.87 % | |||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4 | |||||||||||||||
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 | Resolution: 2.2→15 Å |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Num. obs: 18572 / % possible obs: 89 % / Num. measured all: 43768 / Rmerge(I) obs: 0.086 |
-Processing
Software |
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Refinement | Resolution: 2.2→6 Å / Rfactor Rwork: 0.177 / Rfactor obs: 0.177 / σ(F): 0 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_d / Dev ideal: 3 |