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Yorodumi- PDB-1ql9: FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH RAT TRYPSIN MUTANT X99RT -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ql9 | ||||||
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Title | FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH RAT TRYPSIN MUTANT X99RT | ||||||
Components | TRYPSIN | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / SERINE PROTEINASE | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Collagen degradation / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Collagen degradation / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å | ||||||
Authors | Stubbs, M.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Reconstructing the Binding Site of Factor Xa in Trypsin Reveals Ligand-Induced Structural Plasticity Authors: Reyda, S. / Sohn, C. / Klebe, G. / Rall, K. / Ullmann, D. / Jakubke, H.D. / Stubbs, M.T. #1: Journal: J.Med.Chem. / Year: 1998 Title: Structural and Functional Analyses of Benzamidine-Based Inhibitors in Complex with Trypsin: Implications for the Inhibition of Factor Xa, Tpa, and Urokinase Authors: Renatus, M. / Bode, W. / Huber, R. / Stuerzebecher, J. / Stubbs, M.T. #2: Journal: Curr.Pharm.Des. / Year: 1996 Title: Structural Aspects of Factor Xa Inhibition Authors: Stubbs, M.T. #3: Journal: FEBS Lett. / Year: 1995 Title: Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin Authors: Stubbs, M.T. / Huber, R. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ql9.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ql9.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ql9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/1ql9 ftp://data.pdbj.org/pub/pdb/validation_reports/ql/1ql9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23864.787 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: VARIANT X99RT\: RAT TRYPSIN CONTAINING THE "99"-LOOP OF FACTOR XA Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: PANCREAS / Plasmid: PYT / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P00763, trypsin |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-ZEN / [ |
#5: Water | ChemComp-HOH / |
Compound details | THE 223 AMINO ACIDS OF RAT TRYPSIN ARE IDENTIFIED BY THE RESIDUE NUMBERS OF THE HOMOLOGOUS ...THE 223 AMINO ACIDS OF RAT TRYPSIN ARE IDENTIFIED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.18 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 25MM TRIS PH7, 10MM CACL2, 40% MGSO4, pH 7.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: a single crystal was soaked | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 15, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. obs: 16310 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.456 / Rsym value: 0.456 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 57863 / Rmerge(I) obs: 0.1 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.3→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0
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Refine analyze | Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.34 Å / Total num. of bins used: 20
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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