[English] 日本語
Yorodumi- PDB-4pie: Crystal structure of human adenovirus 2 protease a substrate base... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pie | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human adenovirus 2 protease a substrate based nitrile inhibitor | ||||||
Components |
| ||||||
Keywords | Hydrolase/Hydrolase inhibitor / Adenain / adenovirus / cofactor / pVIc / cysteine protease / Hydrolase-Hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information adenain / nuclear capsid assembly / 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 / cysteine-type peptidase activity / virion component / host cell / viral capsid ...adenain / nuclear capsid assembly / 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 / cysteine-type peptidase activity / 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 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Mac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, C. / Erbel, C. / Hughes, N. / Sirockin, F. / Melkko, S. / Bernardi, A. / Ramage, P. ...Mac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, C. / Erbel, C. / Hughes, N. / Sirockin, F. / Melkko, S. / Bernardi, A. / Ramage, P. / Jarousse, N. / Altmann, E. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2014 Title: Discovery and structure-based optimization of adenain inhibitors. Authors: Mac Sweeney, A. / Grosche, P. / Ellis, D. / Combrink, K. / Erbel, P. / Hughes, N. / Sirockin, F. / Melkko, S. / Bernardi, A. / Ramage, P. / Jarousse, N. / Altmann, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pie.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pie.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 4pie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pie_validation.pdf.gz | 719.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4pie_full_validation.pdf.gz | 722 KB | Display | |
Data in XML | 4pie_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 4pie_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/4pie ftp://data.pdbj.org/pub/pdb/validation_reports/pi/4pie | HTTPS FTP |
-Related structure data
Related structure data | 4pidC 4piqC 4pisC 1nlnS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 23114.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus 2 / Gene: L3 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03252, adenain |
---|---|
#2: Protein/peptide | Mass: 1353.640 Da / Num. of mol.: 1 / Fragment: UNP residues 240-250 / Source method: obtained synthetically / Source: (synth.) Human adenovirus 2 / References: UniProt: P03274 |
-Non-polymers , 5 types, 38 molecules
#3: Chemical | ChemComp-3FO / | ||||||
---|---|---|---|---|---|---|---|
#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.71 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1mM peptide-nitrile inhibitor was added to the protein and incubated for 30 minutes. 0.8M lithium sulphate, 0.1 M sodium acetate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.94→44.4 Å / Num. obs: 14072 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 34.286 Å2 / Rmerge F obs: 0.086 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.059 / Χ2: 1.028 / Net I/σ(I): 19.48 / Num. measured all: 89405 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NLN Resolution: 1.94→40.53 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.13 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.187 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.75 Å2 / Biso mean: 31.634 Å2 / Biso min: 18.43 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→40.53 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.94→1.99 Å / Total num. of bins used: 20
|