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Yorodumi- PDB-1the: CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1the | ||||||
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Title | CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN | ||||||
Components | Cathepsin B | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / THIOL PROTEASE / Glycoprotein / Protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / kininogen binding / cathepsin B / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / thyroid hormone generation / cellular response to thyroid hormone stimulus ...Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / kininogen binding / cathepsin B / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / thyroid hormone generation / cellular response to thyroid hormone stimulus / proteoglycan binding / Neutrophil degranulation / response to amine / response to dexamethasone / decidualization / collagen catabolic process / response to glucose / response to mechanical stimulus / cysteine-type peptidase activity / skeletal muscle tissue development / collagen binding / epithelial cell differentiation / response to cytokine / proteolysis involved in protein catabolic process / peptide binding / protein catabolic process / caveola / sarcolemma / response to organic cyclic compound / response to peptide hormone / autophagy / cellular response to mechanical stimulus / melanosome / peptidase activity / spermatogenesis / neuron apoptotic process / endopeptidase activity / response to ethanol / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / proteolysis / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Huber, C.P. / Jia, Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1995 Title: Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex. Implications for structure-based inhibitor design. Authors: Jia, Z. / Hasnain, S. / Hirama, T. / Lee, X. / Mort, J.S. / To, R. / Huber, C.P. #1: Journal: J.Biol.Chem. / Year: 1990 Title: Crystallization of Recombinant Rat Cathepsin B Authors: Lee, X. / Ahmed, F.R. / Hirama, T. / Huber, C.P. / Rose, D.R. / To, R. / Hasnain, S. / Tam, A. / Mort, J.S. | ||||||
History |
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Remark 700 | SHEET THERE IS A BIFURCATED SHEET IN EACH CHAIN OF THIS ENTRY. A BIFURCATED SHEET IS PRESENTED AS ...SHEET THERE IS A BIFURCATED SHEET IN EACH CHAIN OF THIS ENTRY. A BIFURCATED SHEET IS PRESENTED AS TWO SHEETS WITH ONE OR MORE STRANDS IN COMMON. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1the.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1the.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 1the.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1the_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1the_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1the_validation.xml.gz | 24 KB | Display | |
Data in CIF | 1the_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/1the ftp://data.pdbj.org/pub/pdb/validation_reports/th/1the | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.6405, 0.7349, 0.2229), Vector: |
-Components
#1: Protein | Mass: 28441.562 Da / Num. of mol.: 2 / Mutation: S115A Source method: isolated from a genetically manipulated source Details: RECOMBINANT RAT ENZYME / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CDNA, Ctsb / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00787, cathepsin B #2: Chemical | #3: Water | ChemComp-HOH / | Has protein modification | Y | Sequence details | THE VAL 223 ALA SUBSTITUTION WAS PRESENT IN THE PLASMID SUPPLIED TO DR. J. S. MORT BY DR. SHU CHAN ...THE VAL 223 ALA SUBSTITUTI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.67 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 1, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→14.3 Å / Num. obs: 39749 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.07 |
-Processing
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Refinement | Resolution: 1.9→8 Å / σ(F): 2 Details: RESIDUE ASN 222 OF BOTH CHAINS HAS PHI-PSI ANGLES OUTSIDE THE NORMALLY PERMITTED RANGE BECAUSE ITS SIDECHAIN OXYGEN ATOM IS INVOLVED IN A HYDROGEN BOND WITH THE ADJACENT MAIN-CHAIN N-H 223.
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Displacement parameters | Biso mean: 19.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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