+
Open data
-
Basic information
Entry | Database: PDB / ID: 7q8g | ||||||
---|---|---|---|---|---|---|---|
Title | Peptide ALAASS in complex with human cathepsin V C25S mutant | ||||||
![]() |
| ||||||
![]() | 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 | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 196.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 468.9 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
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.) ![]() ![]() |
---|
-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) |
---|---|
#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 ![](data/chem/img/CL.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.8 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| |||||||||||||||||||||||||
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
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→45.67 Å
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.06→2.1 Å / Total num. of bins used: 20
|