+Open data
-Basic information
Entry | Database: PDB / ID: 3b9f | |||||||||
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Title | 1.6 A structure of the PCI-thrombin-heparin complex | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Michaelis complex / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Hydrolase / Kringle / Protease / Secreted / Serine protease / Zymogen / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information protein C inhibitor-TMPRSS7 complex / protein C inhibitor-TMPRSS11E complex / protein C inhibitor-PLAT complex / protein C inhibitor-PLAU complex / protein C inhibitor-thrombin complex / protein C inhibitor-KLK3 complex / protein C inhibitor-plasma kallikrein complex / seminal vesicle development / protein C inhibitor-coagulation factor V complex / protein C inhibitor-coagulation factor Xa complex ...protein C inhibitor-TMPRSS7 complex / protein C inhibitor-TMPRSS11E complex / protein C inhibitor-PLAT complex / protein C inhibitor-PLAU complex / protein C inhibitor-thrombin complex / protein C inhibitor-KLK3 complex / protein C inhibitor-plasma kallikrein complex / seminal vesicle development / protein C inhibitor-coagulation factor V complex / protein C inhibitor-coagulation factor Xa complex / protein C inhibitor-coagulation factor XI complex / acrosin binding / platelet dense tubular network / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / phosphatidylcholine binding / negative regulation of endopeptidase activity / platelet alpha granule / glycosaminoglycan binding / negative regulation of hydrolase activity / retinoic acid binding / lipid transport / 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 / single fertilization / 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 / 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 / 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 / spermatogenesis / collagen-containing extracellular matrix / blood microparticle / protease binding / 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 / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Li, W. / Adams, T.E. / Huntington, J.A. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex. Authors: Li, W. / Adams, T.E. / Nangalia, J. / Esmon, C.T. / Huntington, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b9f.cif.gz | 171.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b9f.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 3b9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/3b9f ftp://data.pdbj.org/pub/pdb/validation_reports/b9/3b9f | HTTPS FTP |
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-Related structure data
Related structure data | 2ol2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein/peptide , 1 types, 1 molecules L
#1: Protein/peptide | Mass: 5641.175 Da / Num. of mol.: 1 / Fragment: Thrombin light chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00734, thrombin |
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-Protein , 2 types, 2 molecules HI
#2: Protein | Mass: 29764.219 Da / Num. of mol.: 1 / Fragment: Thrombin heavy chain / Mutation: S195A (chymotrypsin numbering) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00734, thrombin |
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#3: Protein | Mass: 44529.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA5, PCI, PLANH3, PROCI / Production host: Escherichia coli (E. coli) / References: UniProt: P05154, UniProt: Q9N2I2*PLUS |
-Sugars , 2 types, 2 molecules
#4: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Polysaccharide | 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 531 molecules
#6: Chemical | #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | Natural variant at this position |
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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: 2.51 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 11% PEG 3350, 0.12M MgSO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2007 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→37.5 Å / Num. all: 102472 / Num. obs: 95914 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.8 / Num. unique all: 13603 / Rsym value: 0.445 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OL2 Resolution: 1.6→30.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1049755.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.1506 Å2 / ksol: 0.358332 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→30.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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