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- PDB-2qnn: HIV-1 protease in complex with a multiple decorated pyrrolidine-b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qnn | ||||||
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Title | HIV-1 protease in complex with a multiple decorated pyrrolidine-based inhibitor | ||||||
![]() | Gag-Pol polyprotein (Pr160Gag-Pol) | ||||||
![]() | HYDROLASE / protein-ligand complex / AIDS / Aspartyl protease / Capsid maturation / Core protein / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Lipoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Phosphorylation / Protease / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc-finger | ||||||
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 / establishment of integrated proviral latency / viral penetration into host nucleus ...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 | ![]() ![]() | ||||||
![]() | Boettcher, J. / Blum, A. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
![]() | ![]() Title: Structure-Guided Design of C2-Symmetric HIV-1 Protease Inhibitors Based on a Pyrrolidine Scaffold. Authors: Blum, A. / Bottcher, J. / Heine, A. / Klebe, G. / Diederich, W.E. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 39.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pqzSC ![]() 2pwcC ![]() 2pwrC ![]() 2qnpC ![]() 2qnqC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 / Fragment: HIV-1 retropepsin Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-QN1 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.25M NaCl, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2007 / Details: Double crystal monochromator wit 2 sets of mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97803 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→25 Å / Num. all: 38945 / Num. obs: 38945 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 4.8 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.71 / Num. unique all: 1863 / Rsym value: 28.7 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: AB INITIO Starting model: pdb entry 2PQZ Resolution: 1.48→10 Å / Num. parameters: 6881 / Num. restraintsaints: 6465 / Isotropic thermal model: isotropic / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 1577 / Occupancy sum non hydrogen: 1698.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→10 Å
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Refine LS restraints |
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