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Yorodumi- PDB-2ynf: HIV-1 Reverse Transcriptase Y188L mutant in complex with inhibito... -
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-Basic information
Entry | Database: PDB / ID: 2ynf | ||||||
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Title | HIV-1 Reverse Transcriptase Y188L mutant in complex with inhibitor GSK560 | ||||||
Components |
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Keywords | HYDROLASE / NNRTI | ||||||
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 | HIV-1 M\:B_HXB2R (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Chong, P. / Sebahar, P. / Youngman, M. / Garrido, D. / Zhang, H. / Stewart, E.L. / Nolte, R.T. / Wang, L. / Ferris, R.G. / Edelstein, M. ...Chong, P. / Sebahar, P. / Youngman, M. / Garrido, D. / Zhang, H. / Stewart, E.L. / Nolte, R.T. / Wang, L. / Ferris, R.G. / Edelstein, M. / Weaver, K. / Mathis, A. / Peat, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Rational Design of Potent Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase. Authors: Chong, P. / Sebahar, P. / Youngman, M. / Garrido, D. / Zhang, H. / Stewart, E.L. / Nolte, R.T. / Wang, L. / Ferris, R.G. / Edelstein, M. / Weaver, K. / Mathis, A. / Peat, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ynf.cif.gz | 414.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ynf.ent.gz | 337.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ynf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ynf_validation.pdf.gz | 829.5 KB | Display | wwPDB validaton report |
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Full document | 2ynf_full_validation.pdf.gz | 838 KB | Display | |
Data in XML | 2ynf_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 2ynf_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/2ynf ftp://data.pdbj.org/pub/pdb/validation_reports/yn/2ynf | HTTPS FTP |
-Related structure data
Related structure data | 2yngC 2ynhC 2yniC 1hmvS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 64845.301 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M\:B_HXB2R (virus) / Plasmid: PKK233-2 VARIANT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
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#2: Protein | Mass: 52238.875 Da / Num. of mol.: 1 / Fragment: RESIDUES 588-1015 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M\:B_HXB2R (virus) / Plasmid: PKK233-2 VARIANT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585 |
-Non-polymers , 4 types, 439 molecules
#3: Chemical | #4: Chemical | ChemComp-TAR / | #5: Chemical | ChemComp-WHU / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | PRESUMED MG IONS D(-)-TARTARIC ACID (TAR): TARTRATE FROM CRYSTALLIZSequence details | Y188L MUTATION POLY HIS TAG ADDED AT THE N-TERMINUS FOR PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 100MM HEPES PH7.5, 10MM SPERMIDINE, 1.1M SODIUM POTASSIUM TARTRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 3, 2008 / Details: BERYLLIUM LENSES |
Radiation | Monochromator: DIAMOND LAUE MONOCHROMATORS SUPPLIED BY JJ X-RAY Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 59250 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.15 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HMV Resolution: 2.36→47.57 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 12.266 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.099 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→47.57 Å
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Refine LS restraints |
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