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Yorodumi- PDB-3dm2: Crystal structure of HIV-1 K103N mutant reverse transcriptase in ... -
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-Basic information
Entry | Database: PDB / ID: 3dm2 | ||||||
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Title | Crystal structure of HIV-1 K103N mutant reverse transcriptase in complex with GW564511. | ||||||
Components |
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Keywords | TRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE / AIDS / NNRTI / GW564511 / DRUG RESISTANCE / K103N mutation / 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 / RNA stem-loop binding / 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: 3.1 Å | ||||||
Authors | Ren, J. / Chamberlain, P.P. / 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 | 3dm2.cif.gz | 203.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dm2.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/3dm2 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/3dm2 | HTTPS FTP |
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-Related structure data
Related structure data | 3dleC 3dlgSC 3dmjC 3dokC 3dolC 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: 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, UniProt: Q74596*PLUS | ||
#3: Chemical | #4: Chemical | ChemComp-GWE / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.17 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 17958 / % possible obs: 90.2 % / Observed criterion σ(I): -1.5 / Redundancy: 2.3 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1742 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3dlg Resolution: 3.1→29.54 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1756563.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: All atoms distant more than 20 Angstrom from the CA atom of Y188 were harmonically restrained during refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19.0281 Å2 / ksol: 0.297243 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→29.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.21 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 10
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Xplor file |
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