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Yorodumi- PDB-1csb: Crystal structure of cathepsin b inhibited with CA030 at 2.1 angs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1csb | ||||||
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Title | Crystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A basis for the design of specific epoxysuccinyl inhibitors | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / PAPAIN-LIKE LYSOSOMAL DICARBOXY-PEPTIDASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization ...cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization / collagen catabolic process / cysteine-type peptidase activity / epithelial cell differentiation / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / regulation of apoptotic process / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / lysosome / symbiont entry into host cell / apical plasma membrane / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Turk, D. / Bode, W. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Crystal structure of cathepsin B inhibited with CA030 at 2.0-A resolution: A basis for the design of specific epoxysuccinyl inhibitors. Authors: Turk, D. / Podobnik, M. / Popovic, T. / Katunuma, N. / Bode, W. / Huber, R. / Turk, V. #1: Journal: Embo J. / Year: 1991 Title: The Refined 2.15 Angstrom X-Ray Crystal Structure of Human Liver Cathepsin B: The Structural Basis for its Specificity Authors: Musil, D. / Zucic, D. / Turk, D. / Engh, R.A. / Mayr, I. / Huber, R. / Popovic, T. / Turk, V. / Towatari, T. / Katunuma, N. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1csb.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1csb.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 1csb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1csb_validation.pdf.gz | 528.5 KB | Display | wwPDB validaton report |
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Full document | 1csb_full_validation.pdf.gz | 537.9 KB | Display | |
Data in XML | 1csb_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 1csb_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/1csb ftp://data.pdbj.org/pub/pdb/validation_reports/cs/1csb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO B 138 / 2: CIS PROLINE - PRO E 138 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.018575, -0.006577, -0.999806), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 D 1 .. D 47 A 1 .. A 47 0.432 M1 E 50 .. E 254 B 50 .. B 254 0.562 M1 F 3 .. F 4 C 3 .. C 4 0.456 | |
-Components
#1: Protein/peptide | Mass: 5213.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: LIVER / Organelle: LYSOSOME / References: UniProt: P07858, cathepsin B #2: Antibody | Mass: 22437.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: LIVER / Organelle: LYSOSOME / References: UniProt: P07858, cathepsin B #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.07 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 21 ℃ / pH: 5 / 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: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 51421 / % possible obs: 79.1 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.098 |
Reflection | *PLUS Highest resolution: 2 Å / Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 64 % |
-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 2 Details: THE MINIMAL ATOMIC TEMPERATURE FACTOR WAS SET TO 5.
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.011 |