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- PDB-3i0r: crystal structure of HIV reverse transcriptase in complex with in... -

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Basic information

Entry
Database: PDB / ID: 3i0r
Titlecrystal structure of HIV reverse transcriptase in complex with inhibitor 3
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE / HIV-1 reverse transcriptase / non-nucleoside inhibition / nucleotidyltrasferase / AIDS / Aspartyl protease / Capsid maturation / Capsid protein / Cell membrane / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Host-virus interaction / Hydrolase / Lipoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / Ribosomal frameshifting / RNA-binding / RNA-directed DNA polymerase / Viral nucleoprotein / Virion / Zinc / Zinc-finger
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 / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / protein processing / 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 / peptidase activity / 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 / DNA binding / zinc ion binding / identical protein 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 / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / 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-RT3 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.98 Å
AuthorsYan, Y. / Prasad, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Substituted tetrahydroquinolines as potent allosteric inhibitors of reverse transcriptase and its key mutants.
Authors: Su, D.S. / Lim, J.J. / Tinney, E. / Wan, B.L. / Young, M.B. / Anderson, K.D. / Rudd, D. / Munshi, V. / Bahnck, C. / Felock, P.J. / Lu, M. / Lai, M.T. / Touch, S. / Moyer, G. / Distefano, D.J. ...Authors: Su, D.S. / Lim, J.J. / Tinney, E. / Wan, B.L. / Young, M.B. / Anderson, K.D. / Rudd, D. / Munshi, V. / Bahnck, C. / Felock, P.J. / Lu, M. / Lai, M.T. / Touch, S. / Moyer, G. / Distefano, D.J. / Flynn, J.A. / Liang, Y. / Sanchez, R. / Prasad, S. / Yan, Y. / Perlow-Poehnelt, R. / Torrent, M. / Miller, M. / Vacca, J.P. / Williams, T.M. / Anthony, N.J.
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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: Reverse transcriptase/ribonuclease H
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0813
Polymers116,6272
Non-polymers4541
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-28 kcal/mol
Surface area45290 Å2
MethodPISA
2
A: Reverse transcriptase/ribonuclease H
B: p51 RT
hetero molecules

A: Reverse transcriptase/ribonuclease H
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,1616
Polymers233,2534
Non-polymers9082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area14870 Å2
ΔGint-78 kcal/mol
Surface area86010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.327, 155.308, 154.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Reverse transcriptase/ribonuclease H / Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid ...Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid protein p7 / NC / Transframe peptide / TF / p6-pol / p6* / Protease / Retropepsin / PR / Reverse transcriptase/ribonuclease H / p66 RT / p51 RT / p15 / Integrase / IN


Mass: 64895.316 Da / Num. of mol.: 1 / Fragment: GAG-POL POLYPROTEIN P66 SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: HXB2 isolate / Gene: gag-pol, HIV-1 pol / Production host: Escherichia coli (E. coli)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: Protein p51 RT / Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid ...Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid protein p7 / NC / Transframe peptide / TF / p6-pol / p6* / Protease / Retropepsin / PR / Reverse transcriptase/ribonuclease H / p66 RT / p51 RT / p15 / Integrase / IN


Mass: 51731.418 Da / Num. of mol.: 1 / Fragment: GAG-POL POLYPROTEIN P51 SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: HXB2 isolate / Gene: gag-pol, HIV-1 pol / Production host: Escherichia coli (E. coli)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase
#3: Chemical ChemComp-RT3 / S-{2-[(2-chloro-4-sulfamoylphenyl)amino]-2-oxoethyl} 6-methyl-3,4-dihydroquinoline-1(2H)-carbothioate / S-(2-{[4-(aminosulfonyl)-2-chlorophenyl]amino}-2-oxoethyl) 6-methyl-3,4-dihydroquinoline-1(2H)-carbothioate


Mass: 453.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20ClN3O4S2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. all: 29440 / Num. obs: 29440 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 20.7
Reflection shellResolution: 2.98→3.11 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.29 / Num. unique all: 2906 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2RF2

2rf2


Resolution: 2.98→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.877 / SU B: 18.29 / SU ML: 0.344 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29505 1494 5.1 %RANDOM
Rwork0.22015 ---
obs0.22392 27922 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.886 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---1.11 Å20 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7794 0 29 0 7823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228037
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.96510925
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9355946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31425.168358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.04151463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6531530
X-RAY DIFFRACTIONr_chiral_restr0.10.21182
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216013
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7081.54758
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35527787
X-RAY DIFFRACTIONr_scbond_it1.57433279
X-RAY DIFFRACTIONr_scangle_it2.8594.53138
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.982→3.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 127 -
Rwork0.275 1858 -
obs--91.26 %

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