+Open data
-Basic information
Entry | Database: PDB / ID: 7q9c | ||||||
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Title | Peptide RLSAKP in complex with human cathepsin V C25A mutant | ||||||
Components |
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Keywords | HYDROLASE / CathepsinV / Peptidyl substrate | ||||||
Function / homology | trifluoroacetic acid Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 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 | 7q9c.cif.gz | 205.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q9c.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q9c_validation.pdf.gz | 503 KB | Display | wwPDB validaton report |
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Full document | 7q9c_full_validation.pdf.gz | 509.4 KB | Display | |
Data in XML | 7q9c_validation.xml.gz | 26 KB | Display | |
Data in CIF | 7q9c_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/7q9c ftp://data.pdbj.org/pub/pdb/validation_reports/q9/7q9c | HTTPS FTP |
-Related structure data
Related structure data | 7q8dC 7q8fC 7q8gC 7q8hC 7q8iC 7q8jC 7q8kC 7q8lC 7q8mC 7q8nC 7q8oC 7q8pC 7q8qC 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 / Protein/peptide , 2 types, 5 molecules AABAPAAPACPBA
#1: Protein | Mass: 24021.936 Da / Num. of mol.: 2 / Mutation: C25A,N179Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella phaffii GS115 (fungus) #2: Protein/peptide | Mass: 696.863 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 5 types, 513 molecules
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-MPD / ( #5: Chemical | ChemComp-GOL / #6: Chemical | #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: 2.76 Å3/Da / Density % sol: 55.37 % |
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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: Oct 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→50 Å / Num. obs: 131146 / % possible obs: 99.8 % / Redundancy: 11.9 % / CC1/2: 1 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.32→1.4 Å / Num. unique obs: 20692 / CC1/2: 0.26 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: 1FH0 Resolution: 1.4→47.05 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.8254 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.7 / Stereochemistry target values: ML
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Solvent computation | Solvent model: MASK FLAT BULK SOLVENT MODEL / Bsol: 37.16 Å2 / ksol: 0.44 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 113.21 Å2 / Biso mean: 24.9 Å2 / Biso min: 8.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→47.05 Å
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LS refinement shell | Resolution: 1.4→1.42 Å / Total num. of bins used: 20
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