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- PDB-3toh: HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Orthorombic C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3toh | ||||||
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Title | HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Orthorombic Crystal form P212121) | ||||||
![]() | Gag-Pol polyprotein | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HIV PR / epoxide / in-crystal reaction / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 / viral penetration into host nucleus / establishment of integrated proviral latency ...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 / viral penetration into host nucleus / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Geremia, S. / Olajuyigbe, F.M. / Demitri, N. | ||||||
![]() | ![]() Title: Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals. Authors: Olajuyigbe, F.M. / Demitri, N. / De Zorzi, R. / Geremia, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.7 KB | Display | ![]() |
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PDB format | ![]() | 74.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 769.3 KB | Display | ![]() |
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Full document | ![]() | 770.4 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tofC ![]() 3togC ![]() 2nmzS S: Starting model for refinement 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: 10740.677 Da / Num. of mol.: 2 / Fragment: UNP Residues 501-599 / Mutation: Q507K L533I L563I C567A C595A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol / Plasmid: pET11A / Production host: ![]() ![]() References: UniProt: P03367, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H #2: Chemical | ChemComp-079 / ( | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | EPOXYDIC INHIBITOR | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Ammonium sulfate 40%, DMSO 10%, sodium citrate 0.25M. pH has been increased through ammonia diffusion, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 11, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.116→42.26 Å / Num. all: 57890 / Num. obs: 69731 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.116→1.17 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.9 / % possible all: 83.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NMZ Resolution: 1.116→42.26 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.083 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.038 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 12.477 Å2
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Refinement step | Cycle: LAST / Resolution: 1.116→42.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.116→1.145 Å / Total num. of bins used: 20
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