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Yorodumi- PDB-1s6q: CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX ... -
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-Basic information
Entry | Database: PDB / ID: 1s6q | ||||||
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Title | CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH JANSSEN-R147681 | ||||||
Components | (POL polyprotein [Contains: Reverse transcriptase]) x 2 | ||||||
Keywords | TRANSFERASE / AIDS / HIV / DRUG DESIGN / REVERSE TRANSCRIPTASE / RT / PROTEIN-INHIBITOR COMPLEX / DRUG RESISTANCE | ||||||
Function / homology | Function and homology information : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / 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 / 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 Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Das, K. / Arnold, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent ...Title: Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 Variants. Authors: Das, K. / Clark, A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, ...Authors: Das, K. / Clark, A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, H. / Lichtenstein, M.A. / Andries, K. / Pauwels, R. / Boyer, P.L. / Clark, P. / Hughes, S.H. / Janssen, P.A. / Arnold, E. #1: Journal: Nat.Struct.Biol. / Year: 1995 Title: Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors Authors: Ding, J. / Das, K. / Moereels, H. / Koymans, L. / Andries, K. / Janssen, P.A.J. / Hughes, S.H. / Arnold, E. #2: Journal: Structure / Year: 1995 Title: Structure of HIV-1 Reverse Transcriptase in a Complex with the Non-Nucleoside Inhibitor Alpha-Apa R 95845 at 2.8 A Resolution Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Jr., A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P.A. ...Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Jr., A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P.A.J. / Smith Jr., R.H. / Kroeger Koepke, M. / Michejda, C.J. / Hughes, S.H. / Arnold, E. #3: Journal: J.Mol.Biol. / Year: 1996 Title: Crystal Structures of 8-Cl and 9-Cl TIBO Complexed with Wild-Type HIV-1 RT and 8-Cl TIBO Complexed with the Tyr181Cys HIV-1 RT Drug-Resistant Mutant Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Jr., A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Jr., R.H. / Kroeger Smith, M.B. / ...Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Jr., A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Jr., R.H. / Kroeger Smith, M.B. / Michejda, C.J. / Hughes, S.H. / Arnold, E. #4: Journal: J.Mol.Biol. / Year: 1998 Title: Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA Template-Primer and an Antibody Fab Fragment at 2.8 A Resolution Authors: Ding, J. / Das, K. / Hsiou, Y. / Sarafianos, S.G. / Clark Jr., A.D. / Jacobo-Molina, A. / Tantillo, C. / Hughes, S.H. / Arnold, E. #5: Journal: Bioorg.Med.Chem.Lett. / Year: 2001 Title: Evolution of Anti-HIV Drug Candidates. Part 3: Diarylpyrimidine (Dapy) Analogues Authors: Ludovici, D.W. / De Corte, B.L. / Kukla, M.J. / Ye, H. / Ho, C.Y. / Lichtenstein, M.A. / Kavash, R.W. / Andries, K. / De Bethune, M. / Azijn, H. / Pauwels, R. / Lewi, P.J. / Heeres, J. / ...Authors: Ludovici, D.W. / De Corte, B.L. / Kukla, M.J. / Ye, H. / Ho, C.Y. / Lichtenstein, M.A. / Kavash, R.W. / Andries, K. / De Bethune, M. / Azijn, H. / Pauwels, R. / Lewi, P.J. / Heeres, J. / Koymans, L.M. / De Jonge, M.R. / Van Aken, K.J. / Daeyaert, F.F. / Das, K. / Arnold, E. / Janssen, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s6q.cif.gz | 209 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s6q.ent.gz | 167.1 KB | Display | PDB format |
PDBx/mmJSON format | 1s6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/1s6q ftp://data.pdbj.org/pub/pdb/validation_reports/s6/1s6q | HTTPS FTP |
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-Related 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: 64500.965 Da / Num. of mol.: 1 / Fragment: P66 SUBUNIT / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: HIV-1 CLONE 12; / Gene: POL / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 ISOLATE / References: UniProt: P03366, RNA-directed DNA polymerase |
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#2: Protein | Mass: 50281.762 Da / Num. of mol.: 1 / Fragment: P51 SUBUNIT / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: HIV-1 CLONE 12 / Gene: POL / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 ISOLATE / References: UniProt: P03366, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-TPB / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.19 % |
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Crystal grow | pH: 6.8 / Details: pH 6.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.921 / Wavelength: 0.921 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.921 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 30428 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 0.325 / % possible all: 78.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.55 Å2 / ksol: 0.23 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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