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- PDB-1gi8: 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: 1gi8 | ||||||
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Title | A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE | ||||||
![]() | (UROKINASE-TYPE PLASMINOGEN ACTIVATOR) x 2 | ||||||
![]() | BLOOD CLOTTING / hydrolase / 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 | ||||||
Function / homology | ![]() u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / 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 | ![]() | 138.3 KB | Display | ![]() |
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PDB format | ![]() | 110.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 703.2 KB | Display | ![]() |
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Full document | ![]() | 710.2 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ghvC ![]() 1ghwC ![]() 1ghxC ![]() 1ghyC ![]() 1ghzC ![]() 1gi0C ![]() 1gi1C ![]() 1gi2C ![]() 1gi3C ![]() 1gi4C ![]() 1gi5C ![]() 1gi6C ![]() 1gi7C ![]() 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
#1: Protein/peptide | Mass: 2708.183 Da / Num. of mol.: 1 / Fragment: SHORT CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Protein | Mass: 27579.473 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: N145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
#3: Chemical | #4: Chemical | ChemComp-BMZ / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.47 % | |||||||||||||||||||||||||||||||||||
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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 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: Jul 19, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→40.95 Å / Num. all: 45525 / Num. obs: 20030 / % possible obs: 44 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.7→1.85 Å / Rmerge(I) obs: 0.327 / Num. unique all: 1930 / % possible all: 31.9 |
Reflection | *PLUS Redundancy: 1.9 % / Num. measured all: 38325 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Details: Only Leu_A9 to Thr_A17 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Thr_B242 are not visible (disordered). Residues ...Details: Only Leu_A9 to Thr_A17 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Thr_B242 are not visible (disordered). Residues simultaneously refined in two or more conformations are: Ile_B17, Thr_B22, Met_B47, Asp_B97, Thr_B139, Arg_B166. Disordered waters are: HOH11 which is close to HOH12; HOH90 which is close to a symmetry-related equivalent of itself; HOH373 which is close to HOH374; HOH497 which is close to a symmetry-related equivalent of itself; HOH681 which is close to HOH682; HOH940 which is close to HOH941, which in turn is close to HOH942; HOH980 which is close to HOH981; HOH1013 which is close to a symmetry-related equivalent of itself; HOH1017 which is close to a symmetry-related equivalent of itself; HOH1031 which is close to a symmetry-related equivalent of itself; No energy terms between citrate 1 and 2 are included because they are hydrogen-bonded to one another via an unusually short hydrogen bond between carboxylate / hydroxyl groups. No energy terms are included among HOH_591, and OgSer195, and O6' of the inhibitor. These atoms form a very short multi-centered hydrogen-bonding network.
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Refinement step | Cycle: LAST / Resolution: 1.75→7 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.204 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 1.83 Å / Rfactor Rfree: 0.261 / Rfactor obs: 0.205 |