[English] 日本語
Yorodumi- PDB-1cpi: REGIOSELECTIVE STRUCTURAL AND FUNCTIONAL MIMICRY OF PEPTIDES. DES... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cpi | ||||||
---|---|---|---|---|---|---|---|
Title | REGIOSELECTIVE STRUCTURAL AND FUNCTIONAL MIMICRY OF PEPTIDES. DESIGN OF HYDROLYTICALLY STABLE CYCLIC PEPTIDOMIMETIC INHIBITORS OF HIV-1 PROTEASE | ||||||
Components |
| ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.05 Å | ||||||
Authors | Martin, J.L. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1995 Title: REGIOSELECTIVE STRUCTURAL AND FUNCTIONAL MIMICRY OF PEPTIDES - DESIGN OF HYDROLYTICALLY-STABLE CYCLIC PEPTIDOMIMETIC INHIBITORS OF HIV-1 PROTEASE. Authors: Abbenante, G. / March, D.R. / Bergman, D.A. / Hunt, P.A. / Garnham, B. / Dancer, R.J. / Martin, J.L. / Fairlie, D.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1cpi.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1cpi.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cpi_validation.pdf.gz | 385.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1cpi_full_validation.pdf.gz | 386.1 KB | Display | |
Data in XML | 1cpi_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1cpi_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/1cpi ftp://data.pdbj.org/pub/pdb/validation_reports/cp/1cpi | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10764.636 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: CHEMICALLY SYNTHESIZED PROTEIN CORRESPONDING TO THE PROTEASE FROM THE HIV-I References: UniProt: P03369 #2: Protein/peptide | | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.94 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.5 / Details: pH 5.5 | |||||||||||||||
Crystal | *PLUS Density % sol: 44 % | |||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 289 K |
---|---|
Diffraction source | Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 10, 1993 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→51 Å / Num. obs: 11539 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.071 |
Reflection | *PLUS Rmerge(I) obs: 0.071 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.05→8 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|