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Yorodumi- PDB-1hap: COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE GGTT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hap | ||||||
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Title | COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE GGTTGGTGTGGTTGG (BASED ON X-RAY MODEL OF DNA) | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR/DNA / COAGULATION / QUADRUPLE HELIX / HYDROLASE-HYDROLASE INHIBITOR-DNA 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 / 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 / positive regulation of cell growth / regulation of cell shape / 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 / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Padmanabhan, K. / Tulinsky, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: An ambiguous structure of a DNA 15-mer thrombin complex. Authors: Padmanabhan, K. / Tulinsky, A. #1: Journal: J.Biol.Chem. / Year: 1993 Title: The Structure of Alpha-Thrombin Inhibited by a 15-mer Single-Stranded DNA Aptamer Authors: Padmanabhan, K. / Padmanabhan, K.P. / Ferrara, J.D. / Sadler, J.E. / Tulinsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hap.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hap.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hap_validation.pdf.gz | 474.1 KB | Display | wwPDB validaton report |
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Full document | 1hap_full_validation.pdf.gz | 546.9 KB | Display | |
Data in XML | 1hap_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 1hap_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/1hap ftp://data.pdbj.org/pub/pdb/validation_reports/ha/1hap | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: residues 328-363 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
#3: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: residues 364-622 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
#4: Chemical | ChemComp-0G6 / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE- ...THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETH |
Sequence details | CHYMOTRYPSIN NUMBERING SYSTEM IS USED FOR THROMBIN, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE ...CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.37 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. obs: 9225 / % possible obs: 57 % / Observed criterion σ(I): 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 15 Å / % possible obs: 68 % / Num. measured all: 21631 / Rmerge(I) obs: 0.097 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 3 Å / % possible obs: 38 % |
-Processing
Software |
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Refinement | Resolution: 2.8→10 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.17 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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