+Open data
-Basic information
Entry | Database: PDB / ID: 7z2i | ||||||
---|---|---|---|---|---|---|---|
Title | TRYPSIN (BOVINE) COMPLEXED WITH compound 4 | ||||||
Components | Serine protease 1 | ||||||
Keywords | HYDROLASE / trypsin / fragment complex / fluorine containing small molecule inhibitor | ||||||
Function / homology | Function and homology information cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | ||||||
Authors | Schiering, N. / Dalvit, C. / Vulpetti, A. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Chemmedchem / Year: 2022 Title: Efficient Screening of Target-Specific Selected Compounds in Mixtures by 19 F NMR Binding Assay with Predicted 19 F NMR Chemical Shifts. Authors: Vulpetti, A. / Lingel, A. / Dalvit, C. / Schiering, N. / Oberer, L. / Henry, C. / Lu, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7z2i.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7z2i.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 7z2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z2i_validation.pdf.gz | 772.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7z2i_full_validation.pdf.gz | 772.7 KB | Display | |
Data in XML | 7z2i_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 7z2i_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/7z2i ftp://data.pdbj.org/pub/pdb/validation_reports/z2/7z2i | HTTPS FTP |
-Related structure data
Related structure data | 7z25C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-DMS / #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-I9O / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.03 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG3350, 0.2 M LISO4, 100 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→33.43 Å / Num. obs: 80517 / % possible obs: 90 % / Redundancy: 5.17 % / Biso Wilson estimate: 10.023 Å2 / Rmerge F obs: 0.049 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.049 / Net I/σ(I): 21.96 / Num. measured all: 416162 |
Reflection shell | Resolution: 1.09→33.43 Å / Redundancy: 2.51 % / Rmerge F obs: 0.015 / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.01 / Num. measured obs: 2943 / Num. possible: 689 / Num. unique obs: 619 / Rrim(I) all: 0.029 / % possible all: 47.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse structure Resolution: 1.09→33.43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.611 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 42.39 Å2 / Biso mean: 9.836 Å2 / Biso min: 3.07 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.09→33.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.09→1.118 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|