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Yorodumi- PDB-1gi7: A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gi7 | ||||||
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Title | A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE | ||||||
Components | (UROKINASE-TYPE PLASMINOGEN ACTIVATOR) x 2 | ||||||
Keywords | 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 | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.79 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gi7.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gi7.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gi7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gi7 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gi7 | HTTPS FTP |
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-Related structure data
Related structure data | 1ghvC 1ghwC 1ghxC 1ghyC 1ghzC 1gi0C 1gi1C 1gi2C 1gi3C 1gi4C 1gi5C 1gi6C 1gi8C 1gi9C 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: 2708.183 Da / Num. of mol.: 1 / Fragment: SHORT CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: CHEM.BIOL. 7, 299-312, 2000 / Plasmid: PPIC9LMWUPA / Production host: Pichia pastoris (fungus) / References: UniProt: P00749 | ||
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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.) Homo sapiens (human) / Description: CHEM.BIOL. 7, 299-312, 2000 / Plasmid: PPIC9LMWUPA / Production host: Pichia pastoris (fungus) / References: UniProt: P00749, u-plasminogen activator | ||
#3: Chemical | ChemComp-120 / | ||
#4: Chemical | #5: 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: 2.06 Å3/Da / Density % sol: 40.15 % | |||||||||||||||||||||||||||||||||||
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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: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→40.95 Å / Num. obs: 21259 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.79→1.87 Å / Num. unique all: 843 / % possible all: 40.1 |
Reflection | *PLUS Num. measured all: 35745 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.79→7.5 Å / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: X-PLOR force field 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: Met B47, Thr B139, Arg B166, Gln B192, Ser B202 Disordered waters are: HOH510 which is close to a symmetry-related equivalent of HOH511; 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.
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Refinement step | Cycle: LAST / Resolution: 1.79→7.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Lowest resolution: 7.5 Å / σ(F): 2.5 / % reflection Rfree: 10 % / Rfactor all: 0.188 / Rfactor obs: 0.185 / Rfactor Rfree: 0.22 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.79 Å / Lowest resolution: 1.87 Å / Rfactor Rfree: 0.22 / Rfactor obs: 0.188 |