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Yorodumi- PDB-1c1s: RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c1s | |||||||||
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Title | RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES | |||||||||
Components | TRYPSIN | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ZN(II)-MEDIATED SERINE PROTEASE INHIBITORS / PH DEPENDENCE / ZN(II) AFFINITY STUCTURE-BASED DRUG DESIGN / SERINE PROTEASE/INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / digestion / serine protease inhibitor complex / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER PLUS REFINEMENT / Resolution: 1.63 Å | |||||||||
Authors | Katz, B.A. / Luong, C. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Recruiting Zn2+ to mediate potent, specific inhibition of serine proteases. Authors: Katz, B.A. / Luong, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c1s.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c1s.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 1c1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/1c1s ftp://data.pdbj.org/pub/pdb/validation_reports/c1/1c1s | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COMPLEXED WITH BIS(5-AMIDINO-2-BENZIMIDAZOLYL)METHANE Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 285 molecules
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | #5: Chemical | ChemComp-BAB / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | HIS91 IS MONOPROTON |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 18 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.1 Details: TRYPSIN-BENZAMIDINE, P3(1) 2 1 WERE GROWN BY VAPOR DIFFUSION, AS DESCRIBED FOR P2(1) 2(1) 2(1) (LARGE CELL) (MANGEL, ET AL., BIOCHEMISTRY 29, 8351-8357, 1990) THE CRYSTAL WAS SOAKED IN A ...Details: TRYPSIN-BENZAMIDINE, P3(1) 2 1 WERE GROWN BY VAPOR DIFFUSION, AS DESCRIBED FOR P2(1) 2(1) 2(1) (LARGE CELL) (MANGEL, ET AL., BIOCHEMISTRY 29, 8351-8357, 1990) THE CRYSTAL WAS SOAKED IN A SOLUTION OF 1.25 M NA2PO4 . 7 H2O, 1.75 M KH2PO4, 2.0 % DMSO, SATURATED IN BABIM OVER A PERIOD OF 5 DAYS WITH SEVERAL REPLACEMENTS OF THE SOAKING SOLUTION., pH 6.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.15 / Method: vapor diffusion, hanging drop / Details: Mangel, W.F., (1990) Biochemistry, 29, 8351. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 16, 1998 / Details: MSC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→36.6 Å / Num. obs: 23706 / % possible obs: 67 % / Observed criterion σ(I): 0.9 / Redundancy: 2.4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.63→1.7 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 1.5 / % possible all: 41.8 |
Reflection | *PLUS Redundancy: 2.4 % / Num. measured all: 56042 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER PLUS REFINEMENT Resolution: 1.63→7.5 Å / Cross valid method: X-PLOR / σ(F): 2 Details: BULK SOLVENT TERMS INCLUDED IN FOB FILE CREATED WITH STANDARD X-PLOR SCRIPT.
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Refinement step | Cycle: LAST / Resolution: 1.63→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.7 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARMALLH3X_TRBAB_PO4_61.P / Topol file: TOPALLH6X_TRBAB_PO4_61.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7.5 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.7 Å / Rfactor Rfree: 0.411 / Rfactor Rwork: 0.186 |