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Yorodumi- PDB-2rki: Crystal Structure of HIV-1 Reverse Transcriptase (RT) in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rki | ||||||
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Title | Crystal Structure of HIV-1 Reverse Transcriptase (RT) in Complex with a triazole derived NNRTI | ||||||
Components | (HIV-1 reverse transcriptase (RT) ...) x 2 | ||||||
Keywords | TRANSFERASE / HIV-1 / Reverse Transcriptase / RT / non-nucleoside reverse transcriptase inhibitor / NNRTI / RNase H / polymerase / virus / AIDS / Aspartyl protease / Capsid maturation / Core protein / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Host-virus interaction / Hydrolase / Lipoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphorylation / Protease / RNA-binding / RNA-directed DNA polymerase / Viral nucleoprotein / Virion / Zinc-finger | ||||||
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 / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Lansdon, E.B. / Kirschberg, T.A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Triazole derivatives as non-nucleoside inhibitors of HIV-1 reverse transcriptase-structure-activity relationships and crystallographic analysis. Authors: Kirschberg, T.A. / Balakrishnan, M. / Huang, W. / Hluhanich, R. / Kutty, N. / Liclican, A.C. / McColl, D.J. / Squires, N.H. / Lansdon, E.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rki.cif.gz | 214.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rki.ent.gz | 169.8 KB | Display | PDB format |
PDBx/mmJSON format | 2rki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/2rki ftp://data.pdbj.org/pub/pdb/validation_reports/rk/2rki | HTTPS FTP |
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-Related structure data
Related structure data | 1vrtS S: Starting model for refinement |
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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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Details | Biological unit is a heterodimer. The p66 domain encompases residues 1-560. The p51 domain encompases the N-terminal portion of the p66 domain residues 1-440. Both subunits are contained in the asymmetric unit. |
-Components
-HIV-1 reverse transcriptase (RT) ... , 2 types, 2 molecules AB
#1: Protein | Mass: 64562.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, RNA-directed DNA polymerase |
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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 1 / Genus: Lentivirus / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, RNA-directed DNA polymerase |
-Non-polymers , 6 types, 310 molecules
#3: Chemical | ChemComp-TT1 / | ||||||
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#4: Chemical | ChemComp-GOL / | ||||||
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-MG / | #8: 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: 3.04 Å3/Da / Density % sol: 59.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: protein was concentrated to 20mg/ml in 10mM Tris pH 7.0, 25mM KCl, 1mM DTT. Protein was mixed 1:1 with resevoir solution containing 1.3M ammonium sulfate, 0.1M sodium cacodylate pH 6.5, 0. ...Details: protein was concentrated to 20mg/ml in 10mM Tris pH 7.0, 25mM KCl, 1mM DTT. Protein was mixed 1:1 with resevoir solution containing 1.3M ammonium sulfate, 0.1M sodium cacodylate pH 6.5, 0.05M sodium malontate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2007 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 60843 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2 / Num. unique all: 2796 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VRT Resolution: 2.3→29.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 148990.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.5929 Å2 / ksol: 0.334493 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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