+Open data
-Basic information
Entry | Database: PDB / ID: 1npw | ||||||
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Title | Crystal structure of HIV protease complexed with LGZ479 | ||||||
Components | POL polyprotein | ||||||
Keywords | HYDROLASE / PROTEASE | ||||||
Function / homology | Function and homology information 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Smith III, A.B. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2003 Title: Design, synthesis, and biological evaluation of monopyrrolinone-based HIV-1 protease inhibitors. Authors: Smith III, A.B. / Cantin, L.D. / Pasternak, A. / Guise-Zawacki, L. / Yao, W. / Charnley, A.K. / Barbosa, J. / Sprengeler, P.A. / Hirschmann, R. / Munshi, S. / Olsen, D.B. / Schleif, W.A. / Kuo, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1npw.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1npw.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 1npw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1npw_validation.pdf.gz | 469.6 KB | Display | wwPDB validaton report |
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Full document | 1npw_full_validation.pdf.gz | 471.8 KB | Display | |
Data in XML | 1npw_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 1npw_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1npw ftp://data.pdbj.org/pub/pdb/validation_reports/np/1npw | HTTPS FTP |
-Related 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 PROTEASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) References: UniProt: P03368, UniProt: P03366*PLUS, HIV-1 retropepsin #2: Chemical | ChemComp-LGZ / | #3: 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: 2.77 Å3/Da / Density % sol: 55.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 600mM NaCl, 100mM Sodium Acetate buffer, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1999 |
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→30 Å / Num. obs: 14186 / % possible obs: 84.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Net I/σ(I): 7.2 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |