[English] 日本語
Yorodumi- PDB-2pgq: Human thrombin mutant C191A-C220A in complex with the inhibitor PPACK -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pgq | ||||||
---|---|---|---|---|---|---|---|
Title | Human thrombin mutant C191A-C220A in complex with the inhibitor PPACK | ||||||
Components |
| ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / serine protease / HYDROLASE-HYDROLASE INHIBITOR 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / 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 / 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 / collagen-containing extracellular matrix / blood microparticle / 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 / signaling receptor binding / serine-type endopeptidase activity / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bush-Pelc, L.A. / Marino, F. / Chen, Z. / Pineda, A.O. / Mathews, F.S. / Di Cera, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Important role of the cys-191 cys-220 disulfide bond in thrombin function and allostery Authors: Bush-Pelc, L.A. / Marino, F. / Chen, Z. / Pineda, A.O. / Mathews, F.S. / Di Cera, E. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Molecular dissection of Na+ binding to thrombin Authors: Pineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z.W. / Mathews, F.S. / Di Cera, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2pgq.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2pgq.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/2pgq ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pgq | HTTPS FTP |
---|
-Related structure data
Related structure data | 2pgbC 1shhS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein/peptide / Protein / Sugars , 3 types, 3 molecules AB
#1: Protein/peptide | Mass: 5280.812 Da / Num. of mol.: 1 / Fragment: residues 319-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: HPC4-PNUT / Cell line (production host): BHK-21 / Organ (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin |
---|---|
#2: Protein | Mass: 29716.090 Da / Num. of mol.: 1 / Fragment: residues 364-622 / Mutation: C191A, C220A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: HPC4-PNUT / Cell line (production host): BHK-21 / Organ (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 308 molecules
#3: Chemical | #4: Chemical | ChemComp-0G6 / | #6: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES: 1) VIA A HEMIKETAL GROUP TO OG SER B ...THE INHIBITOR IS COVALENTLY |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 20% PEG 3350 and 0.2 M Zinc Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 31582 / Num. obs: 31108 / % possible obs: 98.5 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 6.6 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3097 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SHH Resolution: 1.8→25.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 350714.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The authors state that the atoms listed in remark 470 are missing because the residues were mutated to alanine during the refinement.
| ||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.7162 Å2 / ksol: 0.391411 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2
| ||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25.59 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||
Xplor file |
|