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Yorodumi- PDB-2qnq: HIV-1 Protease in complex with a chloro decorated pyrrolidine-bas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qnq | ||||||
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Title | HIV-1 Protease in complex with a chloro decorated pyrrolidine-based inhibitor | ||||||
Components | Gag-Pol polyprotein (Pr160Gag-Pol) | ||||||
Keywords | HYDROLASE / protein-ligand complex / AIDS / Aspartyl protease / Capsid maturation / Core protein / Cytoplasm / 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 / Zinc-finger | ||||||
Function / homology | Function and homology information 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / 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 / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Boettcher, J. / Blum, A. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qnq.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qnq.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qnq_validation.pdf.gz | 917.2 KB | Display | wwPDB validaton report |
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Full document | 2qnq_full_validation.pdf.gz | 919.5 KB | Display | |
Data in XML | 2qnq_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 2qnq_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/2qnq ftp://data.pdbj.org/pub/pdb/validation_reports/qn/2qnq | HTTPS FTP |
-Related structure data
Related structure data | 2pqzSC 2pwcC 2pwrC 2qnnC 2qnpC S: Starting model for refinement 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: 10803.756 Da / Num. of mol.: 2 / Fragment: HIV-1 retropepsin Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: gag-pol / Gene: gag-pol / Plasmid: peT11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(D3)plysS / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | #3: Chemical | ChemComp-QN3 / | #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: 2.66 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.8M NaCl, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 10478 / Num. obs: 10478 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 11 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 5.27 / Num. unique all: 665 / Rsym value: 25.2 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2PQZ Resolution: 2.3→25 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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