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Yorodumi- PDB-1fh0: CRYSTAL STRUCTURE OF HUMAN CATHEPSIN V COMPLEXED WITH AN IRREVERS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fh0 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CATHEPSIN V COMPLEXED WITH AN IRREVERSIBLE VINYL SULFONE INHIBITOR | ||||||
Components | CATHEPSIN V | ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / cathepsin / papain / protease / cancer / HYDROLASE-HYDROLASE inhibitor complex | ||||||
Function / homology | Function and homology information cathepsin V / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / extracellular matrix disassembly / cysteine-type peptidase activity / MHC class II antigen presentation / Degradation of the extracellular matrix ...cathepsin V / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / extracellular matrix disassembly / cysteine-type peptidase activity / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / immune response / cysteine-type endopeptidase activity / serine-type endopeptidase activity / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Somoza, J.R. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structure of human cathepsin V. Authors: Somoza, J.R. / Zhan, H. / Bowman, K.K. / Yu, L. / Mortara, K.D. / Palmer, J.T. / Clark, J.M. / McGrath, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fh0.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fh0.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fh0_validation.pdf.gz | 565.7 KB | Display | wwPDB validaton report |
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Full document | 1fh0_full_validation.pdf.gz | 572.7 KB | Display | |
Data in XML | 1fh0_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1fh0_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/1fh0 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/1fh0 | 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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Details | This enzyme is most likely active as a monomer. |
-Components
#1: Protein | Mass: 24040.959 Da / Num. of mol.: 2 / Mutation: N108Q, N178D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: O60911, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 576.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H40N4O4S Details: This inhibitor is covalently linked to BNS, 4-SULFONYLBENZENE GROUP, to form an irreversible vinyl sulfone inhibitor. References: MePip-Phe-HphVSPh #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Nonpolymer details | INHIBITOR 4-METHYLPIPERAZINE-1-CARBOXYLIC ACID [1-[(3-BENZENESULFONYL-1-PHENETHYLALLYL)CARBAMOYL]-2- ...INHIBITOR 4-METHYLPIPE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.54 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Lithium sulfate, PEG 4000, tris, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 4.5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 22, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. all: 78054 / Num. obs: 78054 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5 % / Rmerge(I) obs: 0.424 / Num. unique all: 3539 / % possible all: 89.9 |
Reflection | *PLUS Highest resolution: 1.6 Å / Num. measured all: 386837 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / % possible obs: 89.9 % / Mean I/σ(I) obs: 3.45 |
-Processing
Software |
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Refinement | Resolution: 1.6→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNX / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.197 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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