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Yorodumi- PDB-5agz: Disubstituted bis-THF moieties as new P2 ligands in non-peptidal ... -
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-Basic information
Entry | Database: PDB / ID: 5agz | ||||||
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Title | Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease Inhibitors (II) | ||||||
Components | PROTEASE | ||||||
Keywords | HYDROLASE / INHIBITOR / RATIONAL DRUG DESIGN / BIS-THF BIS-DIOL | ||||||
Function / homology | Function and homology information symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / 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 ...symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / 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 / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Hohlfeld, K. / Wegner, J.K. / Kesteleyn, B. / Linclau, B. / Unge, J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Disubstituted Bis-Thf Moieties as New P2 Ligands in Non-Peptidal HIV-1 Protease Inhibitors (II). Authors: Hohlfeld, K. / Wegner, J. / Kesteleyn, B. / Linclau, B. / Unge, J. | ||||||
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 | 5agz.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5agz.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 5agz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5agz_validation.pdf.gz | 1002.6 KB | Display | wwPDB validaton report |
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Full document | 5agz_full_validation.pdf.gz | 1008.5 KB | Display | |
Data in XML | 5agz_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 5agz_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/5agz ftp://data.pdbj.org/pub/pdb/validation_reports/ag/5agz | HTTPS FTP |
-Related structure data
Related structure data | 5ah6C 5ah7C 5ah8C 5ah9C 5ahaC 5ahbC 5ahcC 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 / Fragment: ASPARTYL PROTEASE, RESIDUES 501-599 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (Z2/CDC-Z34 ISOLATE) Strain: 99HHP1 (D10) / Variant: Z2/CDC-Z34 ISOLATE / Plasmid: PEXP5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(AI) / References: UniProt: P03366, HIV-1 retropepsin #2: Chemical | #3: Chemical | ChemComp-QHA / ( | #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: 2.7 Å3/Da / Density % sol: 54.53 % / 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: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 3, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→48.31 Å / Num. obs: 74183 / % possible obs: 99.2 % / Observed criterion σ(I): 4 / Redundancy: 4.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NON-PUBLISHED Resolution: 1.2→48.31 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.606 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.045 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→48.31 Å
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