+Open data
-Basic information
Entry | Database: PDB / ID: 2yng | ||||||
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Title | HIV-1 Reverse Transcriptase 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 / 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 | HIV-1 M\:B_HXB2R (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 | 2yng.cif.gz | 428.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yng.ent.gz | 349.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/2yng ftp://data.pdbj.org/pub/pdb/validation_reports/yn/2yng | HTTPS FTP |
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-Related structure data
Related structure data | 2ynfSC 2ynhC 2yniC 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 64895.316 Da / Num. of mol.: 1 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, 665 molecules
#3: Chemical | #4: Chemical | ChemComp-SRT / | #5: Chemical | ChemComp-WHU / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | 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: 58 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 100MM HEPES PH 7.5, 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: Jun 26, 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: 2.12→80 Å / Num. obs: 80302 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.12→2.18 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YNF Resolution: 2.12→78.57 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.601 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.17 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.024 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→78.57 Å
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