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Yorodumi- PDB-7zkm: X-ray structure of the complex between human alpha thrombin and a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zkm | ||||||
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Title | X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form beta | ||||||
Components |
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Keywords | HYDROLASE / Thrombin / Aptamer / Complex / Inhibitor / Coagulation | ||||||
Function / homology | Function and homology information positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / 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 / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / 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 / positive regulation of receptor signaling pathway via JAK-STAT / lipopolysaccharide binding / 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 / 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 / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Troisi, R. / Sica, F. | ||||||
Funding support | 1items
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Citation | Journal: Mol Ther Nucleic Acids / Year: 2022 Title: A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers. Authors: Troisi, R. / Riccardi, C. / Perez de Carvasal, K. / Smietana, M. / Morvan, F. / Del Vecchio, P. / Montesarchio, D. / Sica, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zkm.cif.gz | 181.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zkm.ent.gz | 138.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zkm_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7zkm_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7zkm_validation.xml.gz | 15 KB | Display | |
Data in CIF | 7zkm_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/7zkm ftp://data.pdbj.org/pub/pdb/validation_reports/zk/7zkm | HTTPS FTP |
-Related structure data
Related structure data | 7zklC 7zknC 7zkoC 1ppbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein/peptide / Protein / DNA chain / Sugars , 4 types, 5 molecules LHAB
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin | ||
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin | ||
#3: DNA chain | Mass: 4743.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
-Non-polymers , 6 types, 52 molecules
#5: Chemical | ChemComp-0G6 / | ||||||
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#6: Chemical | ChemComp-NA / | ||||||
#7: Chemical | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 48.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000 20% w/v, 2-propanol 20% v/v, trisodium citrate 0.1 M, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→59.1 Å / Num. obs: 30224 / % possible obs: 99.8 % / Redundancy: 18.1 % / CC1/2: 1 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2→2.04 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1486 / CC1/2: 0.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PPB Resolution: 2→59.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.026 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.9 Å2 / Biso mean: 62.661 Å2 / Biso min: 28.59 Å2
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Refinement step | Cycle: final / Resolution: 2→59.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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