+Open data
-Basic information
Entry | Database: PDB / ID: 7q8g | ||||||
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Title | Peptide ALAASS in complex with human cathepsin V C25S mutant | ||||||
Components |
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Keywords | HYDROLASE / CathepsinV / Peptidyl substrate | ||||||
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 / positive regulation of apoptotic signaling pathway / Endosomal/Vacuolar 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Loboda, J. / Sosnowski, P. / Tusar, L. / Vidmar, R. / Vizovisek, M. / Horvat, J. / Kosec, G. / Impens, F. / Demol, H. / Turk, B. ...Loboda, J. / Sosnowski, P. / Tusar, L. / Vidmar, R. / Vizovisek, M. / Horvat, J. / Kosec, G. / Impens, F. / Demol, H. / Turk, B. / Gevaert, K. / Turk, D. | ||||||
Funding support | Slovenia, 1items
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Citation | Journal: Commun Biol / Year: 2023 Title: Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins. Authors: Tusar, L. / Loboda, J. / Impens, F. / Sosnowski, P. / Van Quickelberghe, E. / Vidmar, R. / Demol, H. / Sedeyn, K. / Saelens, X. / Vizovisek, M. / Mihelic, M. / Fonovic, M. / Horvat, J. / ...Authors: Tusar, L. / Loboda, J. / Impens, F. / Sosnowski, P. / Van Quickelberghe, E. / Vidmar, R. / Demol, H. / Sedeyn, K. / Saelens, X. / Vizovisek, M. / Mihelic, M. / Fonovic, M. / Horvat, J. / Kosec, G. / Turk, B. / Gevaert, K. / Turk, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q8g.cif.gz | 196.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q8g.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/7q8g ftp://data.pdbj.org/pub/pdb/validation_reports/q8/7q8g | HTTPS FTP |
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-Related structure data
Related structure data | 7q8dC 7q8fC 7q8hC 7q8iC 7q8jC 7q8kC 7q8lC 7q8mC 7q8nC 7q8oC 7q8pC 7q8qC 7q9cC 7q9hC 7qffC 7qfhC 7qhjC 7qhkC 1fh0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AABA
#1: Protein | Mass: 24153.025 Da / Num. of mol.: 2 / Mutation: C25S, N179Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSV, CATL2, CTSL2, CTSU, UNQ268/PRO305 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: O60911, cathepsin V |
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-Protein/peptide , 2 types, 2 molecules PAPB
#2: Protein/peptide | Mass: 518.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: Protein/peptide | Mass: 397.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 340 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.85 Å3/Da / Density % sol: 56.8 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / Details: 77 % MPD, 23 % of TRIS, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 35569 / % possible obs: 99.7 % / Redundancy: 13.3 % / CC1/2: 0.998 / Net I/σ(I): 17.77 |
Reflection shell | Resolution: 2.06→2.13 Å / Num. unique obs: 3400 / CC1/2: 0.812 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FH0 Resolution: 2.06→45.67 Å / Cor.coef. Fo:Fc: 0.8839 / Cor.coef. Fo:Fc free: 0.8491 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.5 / Stereochemistry target values: ML
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Solvent computation | Solvent model: MASK FLAT BULK SOLVENT MODEL / Bsol: 25.34 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 180.28 Å2 / Biso mean: 38.03 Å2 / Biso min: 14.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→45.67 Å
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LS refinement shell | Resolution: 2.06→2.1 Å / Total num. of bins used: 20
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