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Open data
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Basic information
Entry | Database: PDB / ID: 1xuh | ||||||
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Title | TRYPSIN-KETO-BABIM-CO+2, PH 8.2 | ||||||
![]() | TRYPSIN | ||||||
![]() | SERINE PROTEASE / COMPLEX / TRYPSIN-COBALT-SMALL MOLECULE LIGAND / DESIGNED SMALL MOLECULE LIGAND WITH MICROMOLAR AFFINITY | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.7 KB | Display | ![]() |
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PDB format | ![]() | 54.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 635.7 KB | Display | ![]() |
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Full document | ![]() | 640.7 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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Similar structure data |
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Links
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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) ![]() ![]() |
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-Non-polymers , 5 types, 129 molecules ![](data/chem/img/CO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BAO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BAO.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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 |
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Processing
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |