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Yorodumi- PDB-4cpt: Macrocyclic Transition-State Mimicking HIV-1 Protease Inhibitors ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cpt | ||||||
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Title | Macrocyclic Transition-State Mimicking HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol | ||||||
Components | PROTEASE | ||||||
Keywords | HYDROLASE / HIV-1 PROTEASE / INHIBITOR / RATIONAL DRUG DESIGN / ENZYME | ||||||
Function / homology | Function and homology information : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | DeRosa, M. / Unge, J. / Motwani, H.V. / Rosenquist, A. / Vrang, L. / Wallberg, H. / Larhed, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Synthesis of P1'-Functionalized Macrocyclic Transition-State Mimicking HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol. Authors: De Rosa, M. / Unge, J. / Motwani, H.V. / Rosenquist, A. / Vrang, L. / Wallberg, H. / Larhed, M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cpt.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cpt.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/4cpt ftp://data.pdbj.org/pub/pdb/validation_reports/cp/4cpt | HTTPS FTP |
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-Related structure data
Related structure data | 4coeC 4cp7C 4cpqC 4cprC 4cpsC 4cpuC 4cpwC 4cpxC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10775.659 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS / Strain: 99HHP1 (D10) / Variant: Z2/CDC-Z34 ISOLATE / Plasmid: PEXP5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: P03366, HIV-1 retropepsin #2: Chemical | #3: Chemical | ChemComp-1T8 / | #4: Water | ChemComp-HOH / | |
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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: 2.69 Å3/Da / Density % sol: 54.23 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.91 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 25, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→31.51 Å / Num. obs: 26209 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NON-PUBLISHED Resolution: 1.7→31.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.872 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 mean: 13.052 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→31.51 Å
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