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Yorodumi- PDB-1hnv: STRUCTURE OF HIV-1 RT(SLASH)TIBO R 86183 COMPLEX REVEALS SIMILARI... -
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-Basic information
Entry | Database: PDB / ID: 1hnv | ||||||
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Title | STRUCTURE OF HIV-1 RT(SLASH)TIBO R 86183 COMPLEX REVEALS SIMILARITY IN THE BINDING OF DIVERSE NONNUCLEOSIDE INHIBITORS | ||||||
Components |
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Keywords | NUCLEOTIDYLTRANSFERASE | ||||||
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 / 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 / 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 / Resolution: 3 Å | ||||||
Authors | Das, K. / Ding, J. / Arnold, E. | ||||||
Citation | 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. / Hughes, S.H. / Arnold, E. #1: Journal: Structure / Year: 1995 Title: Structure of HIV-1 Reverse Transcriptase in a Complex with the Nonnucleoside Inhibitor Alpha-Apa R95845 at 2.8 Angstroms Resolution Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Junior, A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P. ...Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Junior, A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P.A.J. / Smith Junior, R.H. / Koepke, M.K. / Michejda, C.J. / Hughes, S.H. / Arnold, E. #2: Journal: J.Mol.Recog. / Year: 1994 Title: Buried Surface Analysis of HIV-1 Reverse Transcriptase P66(Slash)P51 Heterodimer and its Interaction with DsDNA Template(Slash)Primer Authors: Ding, J. / Jacobo-Molina, A. / Tantillo, C. / Lu, X. / Nanni, R.G. / Arnold, E. #3: Journal: J.Mol.Biol. / Year: 1994 Title: Locations of Anti-Aids Drug Binding Sites and Resistance Mutations in the Three-Dimensional Structure of HIV-1 Reverse Transcriptase: Implications for Mechanisms of Drug Inhibition and Resistance Authors: Tantillo, C. / Ding, J. / Jacobo-Molina, A. / Nanni, R.G. / Boyer, P.L. / Hughes, S.H. / Pauwels, R. / Andries, K. / Janssen, P.A.J. / Arnold, E. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 Angstroms Resolution Shows Bent DNA Authors: Jacobo-Molina, A. / Ding, J. / Nanni, R.G. / Clark Junior, A.D. / Lu, X. / Tantillo, C. / Williams, R.L. / Kamer, G. / Ferris, A.L. / Clark, P. / Hizi, A. / Hughes, S.H. / Arnold, E. #5: Journal: Perspect.Drug Discovery Des. / Year: 1993 Title: Review of HIV-1 Reverse Transcriptase Three-Dimensional Structure: Implications for Drug Design Authors: Nanni, R.G. / Ding, J. / Jacobo-Molina, A. / Hughes, S.H. / Arnold, E. #6: Journal: Nature / Year: 1992 Title: Structure of HIV-1 Reverse Transcriptase(Slash)DNA Complex at 7 Angstroms Resolution Showing Active Site Locations Authors: Arnold, E. / Jacobo-Molina, A. / Nanni, R.G. / Williams, R.L. / Lu, X. / Ding, J. / Clark Junior, A.D. / Zhang, A. / Ferris, A.L. / Clark, P. / Hizi, A. / Hughes, S.H. #7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Crystals of a Ternary Complex of Human Immunodeficiency Virus Type 1 Reverse Transcriptase with a Monoclonal Antibody Fab Fragment and Double-Stranded DNA Diffract X-Rays to 3.5 Angstroms Resolution Authors: Jacobo-Molina, A. / Clark Junior, A.D. / Williams, R.L. / Nanni, R.G. / Clark, P. / Ferris, A.L. / Hughes, S.H. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hnv.cif.gz | 203.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hnv.ent.gz | 162 KB | Display | PDB format |
PDBx/mmJSON format | 1hnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/1hnv ftp://data.pdbj.org/pub/pdb/validation_reports/hn/1hnv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64274.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
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#2: Protein | Mass: 49911.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-TBO / |
Compound details | THE DEFINITION OF SECONDARY STRUCTURAL ELEMENTS IS LARGELY BASED ON PROGRAM PROCHECK AND HYDROGEN- ...THE DEFINITION |
Nonpolymer details | HET GROUP TIBO R 86183 IS TETRAHYDRO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.38 % |
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Crystal grow | *PLUS Method: unknown |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 32514 / % possible obs: 81 % / Observed criterion σ(I): 1 |
-Processing
Software |
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Refinement | Resolution: 3→10 Å / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |