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Yorodumi- PDB-1c1o: RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c1o | ||||||
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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 SERINE PROTEASE/INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER PLUS REFINEMENT / Resolution: 1.4 Å | ||||||
Authors | Katz, B.A. / Luong, C. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Design of potent selective zinc-mediated serine protease inhibitors. Authors: Katz, B.A. / Clark, J.M. / Finer-Moore, J.S. / Jenkins, T.E. / Johnson, C.R. / Ross, M.J. / Luong, C. / Moore, W.R. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c1o.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c1o.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c1o_validation.pdf.gz | 428.7 KB | Display | wwPDB validaton report |
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Full document | 1c1o_full_validation.pdf.gz | 431.6 KB | Display | |
Data in XML | 1c1o_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 1c1o_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/1c1o ftp://data.pdbj.org/pub/pdb/validation_reports/c1/1c1o | HTTPS FTP |
-Related structure data
Related structure data | 1c1nC 1c1pC 1c1qC 1c1rC 1c1tC 1c1uC 1c1vC 1c1wC 1c2dC 1c2eC 1c2fC 1c2gC 1c2hC 1c2iC 1c2jC 1c2kC 1c2lC 1c2mC 1xufC 1xugC 1xuhC 1xuiC 1xujC 1xukC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | HIS91 IS MONOPROTON | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 18 % |
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Crystal grow | pH: 4.98 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 TRANSFERRED TO ...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 TRANSFERRED TO 0.25 M MES, 1.53 M MGSO4 . 7 H2O, PH 4.98 AND SOAKED FOR MANY DAYS DURING WHICH THE SOAKING SOLUTION WAS REPLACED TO REMOVE BOUND BENZAMIDINE. |
Crystal grow | *PLUS Method: unknown |
-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: Apr 15, 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→36.4 Å / Num. obs: 28493 / % possible obs: 71 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.4→1.46 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.6 / % possible all: 35.9 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER PLUS REFINEMENT Resolution: 1.4→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: 1.4→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.46 Å / Total num. of bins used: 8
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Xplor file |
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