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Open data
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Basic information
Entry | Database: PDB / ID: 7q8i | ||||||
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Title | Peptide AVAEKQ in complex with human cathepsin V C25S mutant | ||||||
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![]() | HYDROLASE / CathepsinV / Peptidyl substrate | ||||||
Function / homology | ![]() 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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.3 KB | Display | ![]() |
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Full document | ![]() | 459.7 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q8dC ![]() 7q8fC ![]() 7q8gC ![]() 7q8hC ![]() 7q8jC ![]() 7q8kC ![]() 7q8lC ![]() 7q8mC ![]() 7q8nC ![]() 7q8oC ![]() 7q8pC ![]() 7q8qC ![]() 7q9cC ![]() 7q9hC ![]() 7qffC ![]() 7qfhC ![]() 7qhjC ![]() 7qhkC ![]() 1fh0S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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 / Protein/peptide , 2 types, 4 molecules AABAPAPB
#1: Protein | Mass: 24153.025 Da / Num. of mol.: 2 / Mutation: C25S,N179Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein/peptide | Mass: 645.724 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 409 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MPD / ( #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 77 % MPD, 23 % of 60 mM Tris, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 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: 1.59→50 Å / Num. obs: 75479 / % possible obs: 99.9 % / Redundancy: 13.45 % / CC1/2: 0.999 / Net I/σ(I): 17.91 |
Reflection shell | Resolution: 1.59→1.69 Å / Num. unique obs: 11953 / CC1/2: 0.693 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FH0 Resolution: 1.59→46.74 Å / Cor.coef. Fo:Fc: 0.8854 / Cor.coef. Fo:Fc free: 0.8525 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.2 / Stereochemistry target values: ML
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Solvent computation | Solvent model: MASK FLAT BULK SOLVENT MODEL / Bsol: 24.57 Å2 / ksol: 0.39 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 92.66 Å2 / Biso mean: 23.06 Å2 / Biso min: 8.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→46.74 Å
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LS refinement shell | Resolution: 1.59→1.62 Å / Total num. of bins used: 20
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