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- PDB-1ghv: A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTER... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ghv | |||||||||
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Title | A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / three-centered / very short hydrogen bond / oxyanion hole water / shift of pKa of His57 / structure-based drug design / specificity / urokinase / trypsin / thrombin / Zn+2-mediated inhibition / BLOOD CLOTTING / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
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 / 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 / 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 / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / 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 | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Katz, B.A. / Elrod, K. / Luong, C. / Rice, M. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hatayte, J. / Janc, J. / Link, J. ...Katz, B.A. / Elrod, K. / Luong, C. / Rice, M. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hatayte, J. / Janc, J. / Link, J. / Litvak, J. / Rai, R. / Rice, K. / Sideris, S. / Verner, E. / Young, W. | |||||||||
![]() | ![]() Title: A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site. Authors: Katz, B.A. / Elrod, K. / Luong, C. / Rice, M.J. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hataye, J. / Janc, J. / Link, J. / Litvak, J. / Rai, R. / Rice, K. / Sideris, S. / Verner, E. / Young, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.1 KB | Display | ![]() |
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PDB format | ![]() | 130.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 694.8 KB | Display | ![]() |
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Full document | ![]() | 699.3 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ghwC ![]() 1ghxC ![]() 1ghyC ![]() 1ghzC ![]() 1gi0C ![]() 1gi1C ![]() 1gi2C ![]() 1gi3C ![]() 1gi4C ![]() 1gi5C ![]() 1gi6C ![]() 1gi7C ![]() 1gi8C ![]() 1gi9C 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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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) ![]() |
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#3: Protein/peptide | Mass: 1491.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Protein , 1 types, 1 molecules H
#2: Protein | Mass: 29594.055 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 364-620 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 3 types, 481 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/120.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/120.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NA / |
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#5: Chemical | ChemComp-120 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.29 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.8 Details: PEG 4000, NaCl, pH 7.8, vapor diffusion, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8.2 / PH range high: 7.5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.18 Å / Num. all: 72323 / Num. obs: 25435 / % possible obs: 35.2 % / Observed criterion σ(I): 0.8 / Redundancy: 1.6 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.79→1.87 Å / Rmerge(I) obs: 0.233 / Num. unique all: 975 / % possible all: 40.1 |
Reflection | *PLUS Redundancy: 1.6 % / Num. measured all: 41238 |
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Processing
Software |
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Refinement | Resolution: 1.85→7 Å / σ(F): 1.7 / Stereochemistry target values: X-PLOR force field Details: Lys_H60F, Met_H84, Leu_H130, and Val_H157 were simultaneously refined in two conformations. His_H119 was placed into two conformations. Lys_H60F and Met_H84 were simultaneously refined in ...Details: Lys_H60F, Met_H84, Leu_H130, and Val_H157 were simultaneously refined in two conformations. His_H119 was placed into two conformations. Lys_H60F and Met_H84 were simultaneously refined in two conformations. No density was observed for Trp148, Thr149, Ala149A, Asn149B, Val149C, Gly149D, and Lys149E in the autolysis loop, and these residues are not included in the model. No density was observed for C-terminal residues of the heavy chain following Phe_H245. Residues after Phe_H245 are not included in the model. Disordered waters include: HOH395 which is in a special position. (It 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; The above "waters" correspond to density that is more electron dense than waters. The occupancies were allowed to refine to values greater than unity. HOH436 which is close to HOH437; HOH794 which is close to HOH795; HOH1187 which is close to HOH1188; HOH1215 is close to a symmetry related equivalent of itself. HIS_H91 and His_H119 are MONOPROTONATED ON the epsilon nitrogen
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Refinement step | Cycle: LAST / Resolution: 1.85→7 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7 Å / σ(F): 1.7 / % reflection Rfree: 10 % / Rfactor all: 0.191 / Rfactor obs: 0.18 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 1.93 Å / Rfactor Rfree: 0.235 / Rfactor obs: 0.192 |