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- PDB-1bqi: USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bqi | ||||||
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Title | USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S'-SUBSITES. | ||||||
![]() | PAPAIN | ||||||
![]() | HYDROLASE / SULFHYDRYL PROTEINASE / PAPAIN | ||||||
Function / homology | ![]() papain / serpin family protein binding / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lalonde, J.M. / Zhao, B. / Smith, W.W. / Janson, C.A. / Desjarlais, R.L. / Tomaszek, T.A. / Carr, T.J. / Thompson, S.K. / Yamashita, D.S. / Veber, D.F. / Abdel-Mequid, S.S. | ||||||
![]() | ![]() Title: Use of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites. Authors: LaLonde, J.M. / Zhao, B. / Smith, W.W. / Janson, C.A. / DesJarlais, R.L. / Tomaszek, T.A. / Carr, T.J. / Thompson, S.K. / Oh, H.J. / Yamashita, D.S. / Veber, D.F. / Abdel-Meguid, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.5 KB | Display | ![]() |
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PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bp4C ![]() 1pipS S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 23449.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: METHOXYMETHYLKETONE BOUND NON-COVALENTLY IN S'-SUBSITE Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-SBA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63.62 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1995 |
Radiation | Monochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 11412 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.54→2.64 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.5 / % possible all: 91 |
Reflection | *PLUS Num. measured all: 41190 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PIP Resolution: 2.5→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: GROUP RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: DISORDERED SIDE-CHAINS HAVE THEIR OCCUPANCIES SET TO ZERO IN THE ENTRY, RESIDUES 59, 73, 77, 98, 145
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Displacement parameters | Biso mean: 26.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.31 |