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- PDB-1tmu: Changes in interactions in complexes of hirudin derivatives and h... -
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Basic information
Entry | Database: PDB / ID: 1tmu | ||||||
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Title | Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / PPACK INHIBITOR / Blood coagulation / 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 | ![]() | ||||||
![]() | Priestle, J.P. / Gruetter, M.G. | ||||||
![]() | ![]() 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: ![]() Title: Structure of the Hirugen and Hirulog Complexes of Alpha-Thrombin Authors: Skrzypczak-Jankun, E. / Carperos, V.E. / Ravichandran, K.G. / Tulinsky, A. #2: ![]() Title: Refined Structure of the Hirudin-Thrombin Complex Authors: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R. #3: ![]() 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: ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.5 KB | Display | ![]() |
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PDB format | ![]() | 52.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.6 KB | Display | ![]() |
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Full document | ![]() | 511.9 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO H 37 2: THE FOLLOWING RESIDUES OF THROMBIN HAVE DISORDERED SIDE CHAINS: LYS B 81, LYS B 110, LYS B 149E, AND LYS B 236. 3: RESIDUE TYR H 63 IS SULFATED AS IT IS IN NATIVE HIRUDIN. |
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Components
-Protein/peptide , 2 types, 2 molecules LJ
#1: Protein/peptide | Mass: 3317.741 Da / Num. of mol.: 1 / Fragment: residues 328-363 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: Protein/peptide | Mass: 1491.528 Da / Num. of mol.: 1 / Fragment: residues 62-72 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Protein / Sugars , 2 types, 2 molecules H![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: residues 364-622 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 73 molecules ![](data/chem/img/0G6.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-0G6 / |
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#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETH |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.93 % | |||||||||||||||
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Crystal grow | *PLUS pH: 4 / Method: vapor diffusion, hanging drop | |||||||||||||||
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 Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. obs: 13404 / % possible obs: 93 % / Num. measured all: 35785 / Rmerge(I) obs: 0.08 |
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Processing
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Refinement | Resolution: 2.5→10 Å / Rfactor obs: 0.202 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.202 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_d / Dev ideal: 3.4 |