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- PDB-1pbh: CRYSTAL STRUCTURE OF HUMAN RECOMBINANT PROCATHEPSIN B AT 3.2 ANGS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pbh | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN RECOMBINANT PROCATHEPSIN B AT 3.2 ANGSTROM RESOLUTION | ||||||
![]() | PROCATHEPSIN B | ||||||
![]() | THIOL PROTEASE / CATHEPSIN B / CYSTEINE PROTEASE / PROENZYME / PAPAIN | ||||||
Function / homology | ![]() cathepsin B / peptidase inhibitor complex / endolysosome lumen / thyroid hormone generation / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / collagen catabolic process ...cathepsin B / peptidase inhibitor complex / endolysosome lumen / thyroid hormone generation / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / collagen catabolic process / decidualization / collagen binding / epithelial cell differentiation / MHC class II antigen presentation / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / melanosome / peptidase activity / : / regulation of apoptotic process / ficolin-1-rich granule lumen / lysosome / apical plasma membrane / symbiont entry into host cell / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Podobnik, M. / Turk, D. | ||||||
![]() | ![]() Title: Crystal structures of human procathepsin B at 3.2 and 3.3 Angstroms resolution reveal an interaction motif between a papain-like cysteine protease and its propeptide. Authors: Turk, D. / Podobnik, M. / Kuhelj, R. / Dolinar, M. / Turk, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77 KB | Display | ![]() |
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PDB format | ![]() | 56.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.1 KB | Display | ![]() |
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Full document | ![]() | 381.9 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pbhC ![]() 1hucS 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: 35226.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||
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Crystal grow | pH: 7.3 Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 6000, 0.2 M AMMONIUM SULFATE, 0.1 M HEPES, PH 7.3 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→8 Å / Num. obs: 5151 / % possible obs: 88.5 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.166 / Rsym value: 0.115 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.278 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HUC Resolution: 3.2→10 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 3.2→10 Å
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Software | *PLUS Name: MAIN / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Num. reflection all: 5151 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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