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- PDB-5ah7: Disubstituted bis-THF moieties as new P2 ligands in non-peptidal ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ah7 | ||||||
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Title | Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease Inhibitors (II) | ||||||
![]() | PROTEASE | ||||||
![]() | HYDROLASE / RATIONAL DRUG DESIGN / BIS-THF BIS-DIOL | ||||||
Function / homology | ![]() 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 / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hohlfeld, K. / Wegner, J.K. / Kesteleyn, B. / Linclau, B. / Unge, J. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.1 KB | Display | ![]() |
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PDB format | ![]() | 44.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5agzC ![]() 5ah6C ![]() 5ah8C ![]() 5ah9C ![]() 5ahaC ![]() 5ahbC ![]() 5ahcC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: 99HHP1 (D10) / Plasmid: PEXP5 / Production host: ![]() ![]() References: UniProt: P03366, UniProt: P12499*PLUS, HIV-1 retropepsin #2: Chemical | #3: Chemical | ChemComp-C7J / ( | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 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: 2.2→25.65 Å / Num. obs: 12252 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NON-PUBLISHED Resolution: 1.55→24.42 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.917 / SU B: 1.523 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.09 / 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: 15.262 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→24.42 Å
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