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Yorodumi- PDB-3dok: Crystal structure of K103N mutant HIV-1 reverse transcriptase in ... -
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-Basic information
Entry | Database: PDB / ID: 3dok | ||||||
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Title | Crystal structure of K103N mutant HIV-1 reverse transcriptase in complex with GW678248. | ||||||
Components |
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Keywords | TRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE / AIDS / NNRTI / GW678248 / 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 / 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 / Budding and maturation of HIV virion / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / symbiont-mediated suppression of host gene expression / 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 / 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: 2.9 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 | 3dok.cif.gz | 205.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dok.ent.gz | 163 KB | Display | PDB format |
PDBx/mmJSON format | 3dok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/3dok ftp://data.pdbj.org/pub/pdb/validation_reports/do/3dok | HTTPS FTP |
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-Related structure data
Related structure data | 3dleSC 3dlgC 3dm2C 3dmjC 3dolC S: Starting model for refinement C: citing same article (ref.) |
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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: 64579.871 Da / Num. of mol.: 1 / Fragment: GAG-POL POLYPROTEIN P66 SUBUNIT / Mutation: K103N 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: 51383.969 Da / Num. of mol.: 1 / Fragment: GAG-POL POLYPROTEIN P51 SUBUNIT / Mutation: K103N 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 |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-GWJ / |
#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: 2.35 Å3/Da / Density % sol: 47.63 % |
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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 |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.9→30 Å / Num. obs: 24821 / % possible obs: 99.9 % / Observed criterion σ(I): -1.5 / Redundancy: 8.1 % / Biso Wilson estimate: 87.1 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.2 | |||||||||||||||
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 8 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2443 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DLE Resolution: 2.9→29.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1573805.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: DUE TO THE LOW RATIO BETWEEN THE NUMBER OF REFLECTIONS AND THE NUMBER OF PARAMETERS TO BE REFINED, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS ATOMS MORE THAN 20 ANGSTROM FROM THE CA ...Details: DUE TO THE LOW RATIO BETWEEN THE NUMBER OF REFLECTIONS AND THE NUMBER OF PARAMETERS TO BE REFINED, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS ATOMS MORE THAN 20 ANGSTROM FROM THE CA ATOM OF TYR188) WERE harmonically restrained during refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.0851 Å2 / ksol: 0.295821 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→29.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 10
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Xplor file |
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