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- PDB-3qpj: HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-arm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qpj | ||||||
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Title | HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor | ||||||
![]() | Protease | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Aspartyl Protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 / 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 / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lindemann, I. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Design of a series of novel three-armed pyrrolidine-based inhibitors for HIV-1 protease Authors: Lindemann, I. / Klee, N. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.1 KB | Display | ![]() |
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PDB format | ![]() | 41.3 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 | ![]() 3qbfC ![]() 3qrmC ![]() 3qroC ![]() 3qrsC ![]() 2pqzS C: citing same article ( S: Starting model for refinement |
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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: 10804.808 Da / Num. of mol.: 2 / Mutation: Q7K L33I L63I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET24a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-N4I / | #4: Chemical | ChemComp-DTD / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 700mM NaCl, 100mM Na citrate, 100mM DTT, 3mm NaN3, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 24, 2010 / Details: mirrors |
Radiation | Monochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→30 Å / Num. all: 30793 / Num. obs: 30793 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 17.87 Å2 / Rsym value: 0.1 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.61→1.64 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 1493 / Rsym value: 0.286 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PQZ Resolution: 1.61→20.151 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.16 / σ(F): 0 / Phase error: 18.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.308 Å2 / ksol: 0.404 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.32 Å2 / Biso mean: 20.9214 Å2 / Biso min: 10 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→20.151 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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