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- 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
TitleSTRUCTURE OF HIV-1 RT(SLASH)TIBO R 86183 COMPLEX REVEALS SIMILARITY IN THE BINDING OF DIVERSE NONNUCLEOSIDE INHIBITORS
Components
  • HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
  • HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
KeywordsNUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Retrovirus capsid, C-terminal / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TBO / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsDas, 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
DepositionMar 30, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
B: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5083
Polymers114,1862
Non-polymers3221
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-33 kcal/mol
Surface area48390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.200, 70.200, 105.700
Angle α, β, γ (deg.)90.00, 105.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)


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
#2: Protein HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)


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 / 5-CHLORO-8-METHYL-7-(3-METHYL-BUT-2-ENYL)-6,7,8,9-TETRAHYDRO-2H-2,7,9A-TRIAZA-BENZO[CD]AZULENE-1-THIONE / TBO 8 / TIBO R86183


Mass: 321.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20ClN3S
Compound detailsTHE DEFINITION OF SECONDARY STRUCTURAL ELEMENTS IS LARGELY BASED ON PROGRAM PROCHECK AND HYDROGEN- ...THE DEFINITION OF SECONDARY STRUCTURAL ELEMENTS IS LARGELY BASED ON PROGRAM PROCHECK AND HYDROGEN-BONDING PATTERN. THE NAMES OF SECONDARY STRUCTURAL ELEMENTS WERE BASICALLY KEPT CONSISTENT WITH THAT USED IN JACOBO-MOLINA ET AL. (1993). SOME ASSIGNED BETA STRANDS DO NOT APPEAR TO PARTICIPATE IN BETA SHEETS.
Nonpolymer detailsHET GROUP TIBO R 86183 IS TETRAHYDRO-IMIDAZO(4,5,1-KJ)(1,4- BENZODIAZEPIN-2(1H)-ONE AND THIONE DERIVATIVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.38 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 32514 / % possible obs: 81 % / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 3→10 Å / σ(I): 2
RfactorNum. reflection% reflection
Rfree0.356 --
Rwork0.249 --
obs0.249 26249 83.2 %
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7812 0 21 0 7833
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.93
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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