+Open data
-Basic information
Entry | Database: PDB / ID: 1xuh | ||||||
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Title | TRYPSIN-KETO-BABIM-CO+2, PH 8.2 | ||||||
Components | TRYPSIN | ||||||
Keywords | SERINE PROTEASE / COMPLEX / TRYPSIN-COBALT-SMALL MOLECULE LIGAND / DESIGNED SMALL MOLECULE LIGAND WITH MICROMOLAR AFFINITY | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Katz, B.A. / Clark, J.M. / Finer-Moore, J.S. / Jenkins, T.E. / Johnson, C.R. / Rose, M.J. / Luong, C. / Moore, W.R. / Stroud, R.M. | ||||||
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 | 1xuh.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xuh.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 1xuh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/1xuh ftp://data.pdbj.org/pub/pdb/validation_reports/xu/1xuh | HTTPS FTP |
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-Related structure data
Related structure data | 1c1nC 1c1oC 1c1pC 1c1qC 1c1rC 1c1tC 1c1uC 1c1vC 1c1wC 1c2dC 1c2eC 1c2fC 1c2gC 1c2hC 1c2iC 1c2jC 1c2kC 1c2lC 1c2mC 1xufC 1xugC 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 129 molecules
#2: Chemical | ChemComp-CO / |
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#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-BAO / |
#6: 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: 2.05 Å3/Da / Density % sol: 14.7 % Description: DATA WITH RSYM > 50 % WERE REJECTED ALONG WITH DATA WHOSE VALUES WERE > 3.5 SIGMA FROM THE MEAN FOR EACH SET OF SYMMETRY EQUIVALENTS |
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Crystal grow | pH: 8.2 Details: SYNTHETIC MOTHER LIQUOR = 75% SATURATED MAGNESIUM SULFATE, 25 % 1.0 M TRIS ADJUSTED TO PH 8.2; SATURATED IN KETO-BABIM, 5.0 MM CO+2. COMPLEX PRODUCED BY SOAKING TRYPSIN-BENZAMIDINE CO-CRYSTAL. |
Crystal | *PLUS |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Ambient temp details: ROOM |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.45 Å / Num. obs: 7146 / % possible obs: 76.4 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.128 |
Reflection shell | Resolution: 2.37→2.47 Å / % possible all: 47.1 |
Reflection | *PLUS Highest resolution: 2.37 Å / Lowest resolution: 7.5 Å / Num. measured all: 15007 |
-Processing
Software |
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Refinement | Highest resolution: 2.2 Å / σ(F): 1 Details: RESIDUES SIMULTANEOUSLY REFINED IN TWO OR MORE CONFORMATIONS ARE: SER88, SER110, LEU1123, GLN135, SER170, SER190, GLN192, SER236, ILE242. BULK SOLVENT WAS REFINED. HIS40 AND HIS91 ARE ...Details: RESIDUES SIMULTANEOUSLY REFINED IN TWO OR MORE CONFORMATIONS ARE: SER88, SER110, LEU1123, GLN135, SER170, SER190, GLN192, SER236, ILE242. BULK SOLVENT WAS REFINED. HIS40 AND HIS91 ARE MONOPROTONATED ON THE EPSILON NITROGEN, HIS57 IS MONOPROTONATED ON THE DELTA NITROGEN.
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Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.37 Å / Lowest resolution: 7.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.37 Å / Lowest resolution: 2.47 Å |