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Yorodumi- PDB-3dol: Crystal structure of L100I mutant HIV-1 reverse transcriptase in ... -
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-Basic information
Entry | Database: PDB / ID: 3dol | ||||||
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Title | Crystal structure of L100I mutant HIV-1 reverse transcriptase in complex with GW695634. | ||||||
Components |
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Keywords | TRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE / AIDS / NNRTI / GW695634 / DRUG RESISTANCE / Hydrolase | ||||||
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 / DNA integration / 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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chamberlain, P.P. / Ren, J. / Stammers, D.K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Structural basis for the improved drug resistance profile of new generation benzophenone non-nucleoside HIV-1 reverse transcriptase inhibitors. Authors: Ren, J. / Chamberlain, P.P. / Stamp, A. / Short, S.A. / Weaver, K.L. / Romines, K.R. / Hazen, R. / Freeman, A. / Ferris, R.G. / Andrews, C.W. / Boone, L. / Chan, J.H. / Stammers, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dol.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dol.ent.gz | 165.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/3dol ftp://data.pdbj.org/pub/pdb/validation_reports/do/3dol | HTTPS FTP |
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-Related structure data
Related structure data | 3dleC 3dlgSC 3dm2C 3dmjC 3dokC C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 64594.949 Da / Num. of mol.: 1 / Fragment: GAG-POL POLYPROTEIN P66 SUBUNIT / Mutation: L100I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: HXB2 ISOLATE / Gene: gag-pol / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HXB2 References: UniProt: P04585, UniProt: A7YKL0*PLUS, 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: GAG-POL POLYPROTEIN P51 SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: HXB2 ISOLATE / Gene: gag-pol / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DG2 / References: UniProt: P04585, UniProt: A7YKL0*PLUS | ||||
#3: Chemical | #4: Chemical | ChemComp-GWI / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 24, 2001 | |||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.5→30 Å / Num. obs: 40079 / % possible obs: 100 % / Observed criterion σ(I): -1.5 / Redundancy: 13.8 % / Biso Wilson estimate: 71 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 27.6 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 13 % / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DLG Resolution: 2.5→29.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1962969.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.325 Å2 / ksol: 0.331952 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
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Xplor file |
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