+Open data
-Basic information
Entry | Database: PDB / ID: 7juj | ||||||
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Title | Cruzain bound to Gallinamide inhibitor | ||||||
Components | Cruzipain | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Cysteine protease / Cruzain / Gallinamide / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information cruzipain / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Silva, E.B. / Sharma, V. / Alvarez, L.H. / Gerwick, W.H. / McKerrow, J.H. / Podust, L.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Intramolecular Interactions Enhance the Potency of Gallinamide A Analogues against Trypanosoma cruzi . Authors: Barbosa Da Silva, E. / Sharma, V. / Hernandez-Alvarez, L. / Tang, A.H. / Stoye, A. / O'Donoghue, A.J. / Gerwick, W.H. / Payne, R.J. / McKerrow, J.H. / Podust, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7juj.cif.gz | 502.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7juj.ent.gz | 418.5 KB | Display | PDB format |
PDBx/mmJSON format | 7juj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7juj_validation.pdf.gz | 6.2 MB | Display | wwPDB validaton report |
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Full document | 7juj_full_validation.pdf.gz | 6.2 MB | Display | |
Data in XML | 7juj_validation.xml.gz | 51.5 KB | Display | |
Data in CIF | 7juj_validation.cif.gz | 69.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/7juj ftp://data.pdbj.org/pub/pdb/validation_reports/ju/7juj | HTTPS FTP |
-Related structure data
Related structure data | 7s18C 7s19C 3kkuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22715.133 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: S of CYS25 forms covalent bond with gallinamide / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS / References: UniProt: P25779, cruzipain #2: Chemical | ChemComp-GN9 / #3: Chemical | ChemComp-K / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.91 Å3/Da / Density % sol: 57.67 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9.7 Details: 0.82 M Potassium phosphate, pH 9.7; 0.01 M Betaine hydrochloride |
-Data collection
Diffraction | Mean temperature: 110 K / Ambient temp details: Liquid Nitrogen flow / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 24, 2020 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→9.84 Å / Num. obs: 82446 / % possible obs: 100 % / Observed criterion σ(I): 0.43 / Redundancy: 26.6 % / Biso Wilson estimate: 57.29 Å2 / CC1/2: 0.998 / Rsym value: 0.33 / Χ2: 99.8 / Net I/σ(I): 11.83 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 26.8 % / Mean I/σ(I) obs: 0.43 / Num. unique obs: 6011 / CC1/2: 0.212 / Rsym value: 8.826 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KKU Resolution: 2.2→9.84 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.934 / SU B: 18.884 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.34 Å2 / Biso mean: 64.595 Å2 / Biso min: 35.67 Å2
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Refinement step | Cycle: final / Resolution: 2.2→9.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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