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Yorodumi- PDB-1o2g: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Bindin... -
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-Basic information
Entry | Database: PDB / ID: 1o2g | |||||||||
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Title | Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors | |||||||||
Components |
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Keywords | BLOOD CLOTTING / HYDROLASE/INHIBITOR / serine protease / short hydrogen bond / inhibition mechanism / shift of pKa / trypsin / thrombin / urokinase / factor Xa / hydrolase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / 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 / 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 / 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) Hirudo medicinalis (medicinal leech) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.58 Å | |||||||||
Authors | Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. ...Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, W.F. / Hui, H. / Breitenbucher, G. / Allen, D. / Janc, J. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W.-F. / Hui, H.C. / Breitenbucher, ...Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W.-F. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o2g.cif.gz | 152.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o2g.ent.gz | 121.2 KB | Display | PDB format |
PDBx/mmJSON format | 1o2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/1o2g ftp://data.pdbj.org/pub/pdb/validation_reports/o2/1o2g | HTTPS FTP |
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-Related structure data
Related structure data | 1o2hC 1o2iC 1o2jC 1o2kC 1o2lC 1o2mC 1o2nC 1o2oC 1o2pC 1o2qC 1o2rC 1o2sC 1o2tC 1o2uC 1o2vC 1o2wC 1o2xC 1o2yC 1o2zC 1o30C 1o31C 1o32C 1o33C 1o34C 1o35C 1o36C 1o37C 1o38C 1o39C 1o3aC 1o3bC 1o3cC 1o3dC 1o3eC 1o3fC 1o3gC 1o3hC 1o3iC 1o3jC 1o3kC 1o3lC 1o3mC 1o3nC 1o3oC 1o3pC 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 on special symmetry positions |
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-Components
-Protein/peptide , 2 types, 2 molecules LI
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 328-363 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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#3: Protein/peptide | Mass: 1491.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P28504 |
-Protein , 1 types, 1 molecules H
#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 364-620 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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-Non-polymers , 3 types, 310 molecules
#4: Chemical | ChemComp-NA / |
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#5: Chemical | ChemComp-696 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.6 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 2-propanol, PEG 4000, pH 6.5, vapor diffusion at 298 K, pH 6.50 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 285 K / Ambient temp details: Crystal Cooler |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 4, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→32.19 Å / Num. all: 49555 / Num. obs: 45048 / % possible obs: 90.91 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.58→1.65 Å / % possible obs: 48.34 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.2 / Num. unique all: 7062 |
Reflection | *PLUS Highest resolution: 1.38 Å / Num. obs: 46254 / Num. measured all: 93493 |
Reflection shell | *PLUS Rmerge(I) obs: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.58→7 Å / Cross valid method: THROUGHOUT / σ(F): 0.7 Details: Met_H84, Leu_H130, Val_H157, Pro_H166, and Ile_H174 were simultaneously refined in two conformations. No density was observed for Thr147, Trp148, Thr149, Ala149A, Asn149B, Val149C, Gly149D, ...Details: Met_H84, Leu_H130, Val_H157, Pro_H166, and Ile_H174 were simultaneously refined in two conformations. No density was observed for Thr147, Trp148, Thr149, Ala149A, Asn149B, Val149C, Gly149D, and Lys149E in the autolysis loop, and these residues are not included in the model. In the non-active site peptide inhibitor (acetylhirudin) the tyrosine hydroxyl is sulfonated. HOH477, OgSer195 and O6' of the inhibitor make a 3-centered short hydrogen bond array. Disordered waters include: HOH395 is close to a symmetry related equivalent of itself. HOH396 is close to a symmetry related equivalent of itself. HOH397 is close to a symmetry related equivalent of itself. HIS_H57 IS doubly protonated. HIS_H91 and His_H119 are monoprotonated on the epsilon nitrogen
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Refinement step | Cycle: LAST / Resolution: 1.58→7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.58 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.222 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.58 Å / Lowest resolution: 1.65 Å / Rfactor Rfree: 0.25 |