+Open data
-Basic information
Entry | Database: PDB / ID: 3nbp | ||||||
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Title | HIV-1 reverse transcriptase with aminopyrimidine inhibitor 2 | ||||||
Components |
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Keywords | TRANSFERASE / HIV / RT / REVERSE TRANSCRIPTASE / TRANSFERASE RNA-DIRECTED DNA POLYMERASE / NUCLEOTIDYLTRANSFERASE | ||||||
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 / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / 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 / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 group M subtype B | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.95 Å | ||||||
Authors | Harris, S.F. / Villasenor, A.G. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Discovery of piperidin-4-yl-aminopyrimidines as HIV-1 reverse transcriptase inhibitors. N-benzyl derivatives with broad potency against resistant mutant viruses. Authors: Kertesz, D.J. / Brotherton-Pleiss, C. / Yang, M. / Wang, Z. / Lin, X. / Qiu, Z. / Hirschfeld, D.R. / Gleason, S. / Mirzadegan, T. / Dunten, P.W. / Harris, S.F. / Villasenor, A.G. / Hang, J.Q. ...Authors: Kertesz, D.J. / Brotherton-Pleiss, C. / Yang, M. / Wang, Z. / Lin, X. / Qiu, Z. / Hirschfeld, D.R. / Gleason, S. / Mirzadegan, T. / Dunten, P.W. / Harris, S.F. / Villasenor, A.G. / Hang, J.Q. / Heilek, G.M. / Klumpp, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nbp.cif.gz | 206.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nbp.ent.gz | 164.3 KB | Display | PDB format |
PDBx/mmJSON format | 3nbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nbp_validation.pdf.gz | 718.6 KB | Display | wwPDB validaton report |
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Full document | 3nbp_full_validation.pdf.gz | 733.8 KB | Display | |
Data in XML | 3nbp_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 3nbp_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/3nbp ftp://data.pdbj.org/pub/pdb/validation_reports/nb/3nbp | 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H | ||||
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#2: Protein | Mass: 51399.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04585 | ||||
#3: Chemical | #4: Chemical | ChemComp-JGZ / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 1.4 M Na-Malonate, 50mM KPO4 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: BL9-1 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2006 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. all: 29914 / Num. obs: 28615 / % possible obs: 95.66 % / Redundancy: 6.6 % / Biso Wilson estimate: 77.8 Å2 / Rsym value: 0.115 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.48 / Num. unique all: 2165 / Rsym value: 0.712 / % possible all: 73.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.95→25.14 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.8819 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 79.67 Å2
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Refine analyze | Luzzati coordinate error obs: 0.405 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→25.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.06 Å / Total num. of bins used: 14
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