+Open data
-Basic information
Entry | Database: PDB / ID: 30 | ||||||
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Title | HIV-RT with non-nucleoside inhibitor annulated pyrazole 2 | ||||||
Components | (Gag-Pol polyprotein) x 2 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / host multivesicular body / protein processing / 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 / peptidase activity / 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 / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Harris, S.F. / Villasenor, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Design of annulated pyrazoles as inhibitors of HIV-1 reverse transcriptase Authors: Sweeney, Z.K. / Harris, S.F. / Arora, S.F. / Javanbakht, H. / Li, Y. / Fretland, J. / Davidson, J.P. / Billedeau, J.R. / Gleason, S.K. / Hirschfeld, D. / Kennedy-Smith, J.J. / Mirzadegan, T. ...Authors: Sweeney, Z.K. / Harris, S.F. / Arora, S.F. / Javanbakht, H. / Li, Y. / Fretland, J. / Davidson, J.P. / Billedeau, J.R. / Gleason, S.K. / Hirschfeld, D. / Kennedy-Smith, J.J. / Mirzadegan, T. / Roetz, R. / Smith, M. / Sperry, S. / Suh, J.M. / Wu, J. / Tsing, S. / Villasenor, A.G. / Paul, A. / Su, G. / Heilek, G. / Hang, J.Q. / Zhou, A.S. / Jernelius, J.A. / Zhang, F.J. / Klumpp, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e01.cif.gz | 198.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e01.ent.gz | 159 KB | Display | PDB format |
PDBx/mmJSON format | 3e01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e01_validation.pdf.gz | 732 KB | Display | wwPDB validaton report |
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Full document | 3e01_full_validation.pdf.gz | 751.7 KB | Display | |
Data in XML | 3e01_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 3e01_validation.cif.gz | 46.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/3e01 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/3e01 | 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: 64710.121 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 588-1148 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
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#2: Protein | Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 588-1027 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
#3: Chemical | ChemComp-PZ2 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 1.4 M SODIUM MALONATE, 50 mM POTASSIUM PHOSPHATE pH 7.2, 5% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979462 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979462 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→46.6 Å / Num. all: 29541 / Num. obs: 27713 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 83.1 Å2 / Rsym value: 0.085 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.59 / Num. unique all: 1878 / Rsym value: 0.56 / % possible all: 64.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→46.83 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 84.903 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→46.83 Å
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Refine LS restraints |
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