[English] 日本語
Yorodumi- PDB-4wx7: Crystal structure of adenovirus 8 protease with a nitrile inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wx7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of adenovirus 8 protease with a nitrile inhibitor | ||||||
Components |
| ||||||
Keywords | HYDROLASE / cysteine protease / inhibitor / covalent | ||||||
Function / homology | Function and homology information adenain / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / virion component / host cell / viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity ...adenain / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / virion component / host cell / viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / host cell nucleus / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | Human adenovirus D serotype 8 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Grosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K. ...Grosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K. / Jarousse, N. / Altmann, E. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2015 Title: Structure-based design and optimization of potent inhibitors of the adenoviral protease. Authors: Grosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K.D. / Jarousse, N. / Altmann, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wx7.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wx7.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 4wx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wx7_validation.pdf.gz | 898.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4wx7_full_validation.pdf.gz | 910.1 KB | Display | |
Data in XML | 4wx7_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 4wx7_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/4wx7 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/4wx7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
#1: Protein | Mass: 22993.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus D serotype 8 / Gene: L3 / Production host: Escherichia coli (E. coli) / References: UniProt: B9A5C1 #2: Protein/peptide | Mass: 1370.691 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human adenovirus D serotype 8 / References: UniProt: B9A5F5 #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.93 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Reservoir: 20% w/v PEG3350, 0.2 M Na citrate Crystallization Protein Solution = 20 mg/ml adenain in 20 mM Tris, 100 mM NaCl, pH 7.6, nominal 5 mM inhibitor (precipitate) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→35.33 Å / Num. obs: 15648 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.37 % / Biso Wilson estimate: 30.486 Å2 / Rmerge F obs: 0.979 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.153 / Χ2: 0.909 / Net I/σ(I): 6.73 / Num. measured all: 52847 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→35.33 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.78 / SU B: 15.904 / SU ML: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 65.63 Å2 / Biso mean: 23.436 Å2 / Biso min: 9.26 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→35.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
|