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- PDB-2rf2: HIV reverse transcriptase in complex with inhibitor 7e (NNRTI) -

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Basic information

Entry
Database: PDB / ID: 2rf2
TitleHIV reverse transcriptase in complex with inhibitor 7e (NNRTI)
Components(Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (p66 RT)) x 2
KeywordsTRANSFERASE / HIV-1 revers transcriptase / AIS / non-nucleoside inhibition / nucleotidyltransferase / AIDS / Aspartyl protease / Capsid maturation / Core protein / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Host-virus interaction / Hydrolase / Lipoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleus / Phosphorylation / Protease / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / Assembly Of The HIV Virion / exoribonuclease H / exoribonuclease H activity / Budding and maturation of HIV virion / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / peptidase activity / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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-MRX / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYan, Y. / Prasad, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Novel indole-3-sulfonamides as potent HIV non-nucleoside reverse transcriptase inhibitors (NNRTIs).
Authors: Zhao, Z. / Wolkenberg, S.E. / Lu, M. / Munshi, V. / Moyer, G. / Feng, M. / Carella, A.V. / Ecto, L.T. / Gabryelski, L.J. / Lai, M.T. / Prasad, S.G. / Yan, Y. / McGaughey, G.B. / Miller, M.D. ...Authors: Zhao, Z. / Wolkenberg, S.E. / Lu, M. / Munshi, V. / Moyer, G. / Feng, M. / Carella, A.V. / Ecto, L.T. / Gabryelski, L.J. / Lai, M.T. / Prasad, S.G. / Yan, Y. / McGaughey, G.B. / Miller, M.D. / Lindsley, C.W. / Hartman, G.D. / Vacca, J.P. / Williams, T.M.
History
DepositionSep 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (p66 RT)
B: Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (p66 RT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9993
Polymers116,6272
Non-polymers3721
Water12,791710
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.290, 155.810, 155.860
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 (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (p66 RT)


Mass: 64895.316 Da / Num. of mol.: 1 / Fragment: HIV-1 reverse transcriptase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: HXB2 ISOLATE / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, RNA-directed DNA polymerase
#2: Protein Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (p66 RT)


Mass: 51731.418 Da / Num. of mol.: 1 / Fragment: HIV-1 reverse transcriptase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: HXB2 ISOLATE / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, RNA-directed DNA polymerase
#3: Chemical ChemComp-MRX / 5-bromo-3-(pyrrolidin-1-ylsulfonyl)-1H-indole-2-carboxamide


Mass: 372.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14BrN3O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: sodium citrate, pH 6.1, VAPOR DIFFUSION, SITTING 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: May 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 57768 / Num. obs: 57711 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 51.041 Å2 / Rsym value: 0.11 / Net I/σ(I): 17.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.64 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER-TNT2.1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1RTJ

1rtj


Resolution: 2.4→15.77 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2916 5.07 %RANDOM
Rwork0.1852 ---
obs0.1888 57465 99.17 %-
Displacement parametersBiso mean: 45.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.50916312 Å20 Å20 Å2
2---0.01086885 Å20 Å2
3----0.49829426 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7862 0 21 710 8593
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01180952
X-RAY DIFFRACTIONt_angle_deg1.285109352
X-RAY DIFFRACTIONt_dihedral_angle_d26.09916900
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.012252
X-RAY DIFFRACTIONt_gen_planes0.01711105
X-RAY DIFFRACTIONt_it1.943809520
X-RAY DIFFRACTIONt_nbd0.0611935
LS refinement shellResolution: 2.4→2.53 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.321 455 5.13 %
Rwork0.2339 8412 -
all0.2383 8867 -
obs--99.17 %

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