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Yorodumi- PDB-1gjd: ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER19... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gjd | ||||||
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Title | ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER190 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS | ||||||
Components | (UROKINASE-TYPE PLASMINOGEN ACTIVATORUrokinase) x 2 | ||||||
Keywords | BLOOD CLOTTING / hydrolase / selectivity at S1 / H2O displacement / uPA / tPA / Ser190/Ala190 protease / structure-based drug design | ||||||
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 / tertiary granule membrane / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / specific granule membrane / regulation of cell adhesion / 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 / FOURIER SYNTHESIS / Resolution: 1.75 Å | ||||||
Authors | Katz, B.A. / Sprengeler, P.A. / Luong, C. / Verner, E. / Spencer, J.R. / Breitenbucher, J.G. / Hui, H. / McGee, D. / Allen, D. / Martelli, A. / Mackman, R.L. | ||||||
Citation | Journal: Chem.Biol. / Year: 2001 Title: Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets. Authors: Katz, B.A. / Sprengeler, P.A. / Luong, C. / Verner, E. / Elrod, K. / Kirtley, M. / Janc, J. / Spencer, J.R. / Breitenbucher, J.G. / Hui, H. / McGee, D. / Allen, D. / Martelli, A. / Mackman, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gjd.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gjd.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/1gjd ftp://data.pdbj.org/pub/pdb/validation_reports/gj/1gjd | HTTPS FTP |
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-Related structure data
Related structure data | 1gj4C 1gj5C 1gj6C 1gj7C 1gj8C 1gj9C 1gjaC 1gjbC 1gjcC 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: P.PASTORIS / Plasmid: PPIC9LMWUPA / Production host: Escherichia coli (E. coli) / References: UniProt: P00749 | ||||||
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#2: Protein | Mass: 28435.428 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: P.PASTORIS / Plasmid: PPIC9LMWUPA / Production host: Escherichia coli (E. coli) / References: UniProt: P00749, u-plasminogen activator | ||||||
#3: Chemical | #4: Chemical | ChemComp-136 / | #5: Water | ChemComp-HOH / | Sequence details | For the listed sequence conflict, See Chem.Biol. 7, 299-312, 2000 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.56 % | ||||||||||||||||||||||||||||||
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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: 7.4 / Method: vapor diffusion, hanging drop / Details: Katz, B.A., (2000) Chem.Biol., 7, 299. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 24, 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: 1.36→23.03 Å / Num. all: 53462 / Num. obs: 19907 / % possible obs: 37.2 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.7→1.85 Å / Rmerge(I) obs: 0.225 / Num. unique all: 2072 / % possible all: 27.9 |
Reflection | *PLUS Num. obs: 16414 |
Reflection shell | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 1.83 Å |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→7 Å / Cross valid method: THROUGHOUT / σ(F): 1.8 / Stereochemistry target values: X-PLOR force field Details: Only Pro_A5 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 Pro_A5 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, Met_B81, Ser_B95, Glu_B110B, Thr_B139, Met_B207, Leu_B235 Disordered waters are: HOH516 which is close to HOH517 HOH1081 which is close to HOH1082 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: 1.75→7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / % reflection Rfree: 10 % / Rfactor obs: 0.166 / Rfactor Rfree: 0.188 / Rfactor Rwork: 0.166 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 1.83 Å / Rfactor Rwork: 0.18 / Rfactor obs: 0.18 |