+Open data
-Basic information
Entry | Database: PDB / ID: 6pxq | ||||||
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Title | Crystal structure of human thrombin mutant D194A | ||||||
Components |
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Keywords | HYDROLASE / trypsin-like proteases / ionic interaction | ||||||
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 / 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) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Stojanovski, B. / Chen, Z. / Koester, S.K. / Pelc, L.A. / Di Cera, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2019 Title: Role of the I16-D194 ionic interaction in the trypsin fold. Authors: Stojanovski, B.M. / Chen, Z. / Koester, S.K. / Pelc, L.A. / Di Cera, E. #1: Journal: EMBO j. / Year: 1989 Title: THE REFINED 1.9 A 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pxq.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pxq.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 6pxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/6pxq ftp://data.pdbj.org/pub/pdb/validation_reports/px/6pxq | HTTPS FTP |
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-Related structure data
Related structure data | 6pxjC 1ppbS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein/peptide | Mass: 3791.204 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin |
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#2: Protein | Mass: 29736.211 Da / Num. of mol.: 1 / Mutation: D194A Source method: isolated from a genetically manipulated source Details: D-A, D194 mutant to A194 WTANVGKG were disordered in the structure. DEGK were disordered in the structure. GE were disordered in the structure. Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin |
#3: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 200 mM di-Na phosphate and 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→66.63 Å / Num. obs: 10857 / % possible obs: 94.8 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 12.2 % / Rsym value: 0.147 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 4.6 % / Num. unique obs: 399 / Rsym value: 0.435 / % possible all: 73.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PPB Resolution: 2.8→66.63 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.882 / SU B: 28.651 / SU ML: 0.465 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.031 / ESU R Free: 0.398 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 195.26 Å2 / Biso mean: 88.695 Å2 / Biso min: 53.85 Å2
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Refinement step | Cycle: final / Resolution: 2.8→66.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Rfactor Rfree error: 0
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