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- PDB-2b5t: 2.1 Angstrom structure of a nonproductive complex between antithr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2b5t | |||||||||
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Title | 2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules | |||||||||
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![]() | BLOOD CLOTTING / Blood coagulation | |||||||||
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 / 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 / Post-translational protein phosphorylation / 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 / 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 / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / protease binding / 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 / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Johnson, D.J. / Li, W. / Luis, S.A. / Carrell, R.W. / Huntington, J.A. | |||||||||
![]() | ![]() Title: Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation. Authors: Johnson, D.J. / Langdown, J. / Li, W. / Luis, S.A. / Baglin, T.P. / Huntington, J.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243.6 KB | Display | ![]() |
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PDB format | ![]() | 190.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1t1fC ![]() 2behC ![]() 1nq9S ![]() 1ppbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein/peptide , 1 types, 2 molecules AC
#1: Protein/peptide | Mass: 5641.175 Da / Num. of mol.: 2 / Fragment: thrombin light chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein , 2 types, 3 molecules BDI
#2: Protein | Mass: 29764.219 Da / Num. of mol.: 2 / Fragment: thrombin heavy chain, serine protease / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | | Mass: 49091.066 Da / Num. of mol.: 1 / Mutation: I15M, S137A, V317C, T401C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 5 types, 6 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)- ...2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-sulfonato-beta-D-glucopyranose-(1-4)-2,3-di-O-methyl-6-O-sulfonato-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3-di-O-methyl-6-O-sulfonato-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-alpha-L-idopyranuronic acid-(1-4)-methyl 3-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranoside | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: 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 #10: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 407 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-SO4 / #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG3350, glycerol, ammonium sulfate, (crystallized with NaCl and tris, but not in cryoprotectant), pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35.7 Å / Num. all: 72517 / Num. obs: 71994 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.6 / Num. unique all: 9773 / Rsym value: 0.44 / % possible all: 85.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PPB and 1NQ9 Resolution: 2.1→35.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1108259.95 / Data cutoff high rms absF: 1108259.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.7278 Å2 / ksol: 0.33387 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→35.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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