+Open data
-Basic information
Entry | Database: PDB / ID: 3h6s | ||||||
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Title | Structure of clitocypin - cathepsin V complex | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / cathepsin / clitocypin / Kunitz inhibitor / cysteine protease / Disulfide bond / Glycoprotein / Hydrolase / Lysosome / Protease / Thiol protease / Zymogen / 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 / cysteine-type endopeptidase inhibitor activity / 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 ...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 / cysteine-type endopeptidase inhibitor activity / 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 / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / immune response / serine-type endopeptidase activity / cysteine-type endopeptidase activity / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Clitocybe nebularis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Renko, M. / Sabotic, J. / Brzin, J. / Turk, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Versatile loops in mycocypins inhibit three protease families. Authors: Renko, M. / Sabotic, J. / Mihelic, M. / Brzin, J. / Kos, J. / Turk, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h6s.cif.gz | 307.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h6s.ent.gz | 258.5 KB | Display | PDB format |
PDBx/mmJSON format | 3h6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h6s_validation.pdf.gz | 516.8 KB | Display | wwPDB validaton report |
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Full document | 3h6s_full_validation.pdf.gz | 562.6 KB | Display | |
Data in XML | 3h6s_validation.xml.gz | 68.9 KB | Display | |
Data in CIF | 3h6s_validation.cif.gz | 95.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/3h6s ftp://data.pdbj.org/pub/pdb/validation_reports/h6/3h6s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | The biological unit is one complex between cathepsin V and clitocypin. |
-Components
#1: Protein | Mass: 24087.053 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL2, CATL2, CTSU, CTSV, UNQ268/PRO305 / Production host: Pichia pastoris (fungus) / References: UniProt: O60911, cathepsin V #2: Protein | Mass: 16914.688 Da / Num. of mol.: 4 / Mutation: I82M, L89M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clitocybe nebularis (fungus) / Gene: clt5 / Production host: Pichia pastoris (fungus) / References: UniProt: Q3Y9I6 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | RESIDUE 25(CYC) IN CATHEPSIN L2 IS MODIFIED. CATHEPSIN L2 WAS TREATED WITH METHYL ...RESIDUE 25(CYC) IN CATHEPSIN L2 IS MODIFIED. CATHEPSIN L2 WAS TREATED WITH METHYL METHANETHI | |
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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: 2.54 Å3/Da / Density % sol: 51.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 0 Details: 0.4 M Li2SO4, 12% PEG800, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 20, 2008 |
Radiation | Monochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→50 Å / Num. obs: 81809 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.037 / Χ2: 0.709 / Net I/σ(I): 43.89 |
Reflection shell | Resolution: 2.22→2.26 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.171 / Num. unique all: 3148 / Χ2: 0.94 / % possible all: 76.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→50 Å / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.839 / SU R Cruickshank DPI: 0.273 / SU Rfree: 0.218 / Isotropic thermal model: random / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 95.66 Å2 / Biso mean: 32.282 Å2 / Biso min: 3.56 Å2 | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.26 Å
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