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- PDB-1tv6: HIV-1 Reverse Transcriptase Complexed with CP-94,707 -

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Basic information

Entry
Database: PDB / ID: 1tv6
TitleHIV-1 Reverse Transcriptase Complexed with CP-94,707
Components
  • reverse transcriptase p51 subunit
  • reverse transcriptase p66 subunit
KeywordsTRANSFERASE
Function / homology
Function and homology information


symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / 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 ...symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / 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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / 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. / Ribonuclease H superfamily / Aspartic peptidase domain 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-CP9 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsPata, J.D. / Stirtan, W.G. / Goldstein, S.W. / Steitz, T.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structure of HIV-1 reverse transcriptase bound to an inhibitor active against mutant RTs resistant to other non-nucleoside inhibitors
Authors: Pata, J.D. / Stirtan, W.G. / Goldstein, S.W. / Steitz, T.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1
Authors: Smerdon, S.J. / Jaeger, J. / Wang, J. / Kohlstaedt, L.A. / Chirino, A.J. / Friedman, J.M. / Rice, P.A. / Steitz, T.A.
#2: Journal: Science / Year: 1992
Title: Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor
Authors: Kohlstaedt, L.A. / Wang, J. / Friedman, J.M. / Rice, P.A. / Steitz, T.A.
History
DepositionJun 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The reference for the bound inhibitor (CP-94,707): Goldstein, S.W., Stirtan, W.G. & ...HETEROGEN The reference for the bound inhibitor (CP-94,707): Goldstein, S.W., Stirtan, W.G. & Sherer, B.A. (2001) US Patent 6,242,461 (Pfizer, Inc.), CAN 135:19641.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: reverse transcriptase p66 subunit
B: reverse transcriptase p51 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2613
Polymers115,8882
Non-polymers3721
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-25 kcal/mol
Surface area45960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.91, 69.04, 104.33
Angle α, β, γ (deg.)90.00, 106.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein reverse transcriptase p66 subunit


Mass: 64517.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Gene: POL / Plasmid: pKRT / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P03366, sulfate adenylyltransferase
#2: Protein reverse transcriptase p51 subunit


Mass: 51371.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Gene: POL / Plasmid: pKRT / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P03366, sulfate adenylyltransferase
#3: Chemical ChemComp-CP9 / 3-[4-(2-METHYL-IMIDAZO[4,5-C]PYRIDIN-1-YL)BENZYL]-3H-BENZOTHIAZOL-2-ONE / CP-94,707


Mass: 372.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16N4OS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 65 %
Crystal growpH: 7
Details: 50 mM bis-Tris-propane, 100 mM ammonium sulfate, 0.2% (w/v) beta-octylglucoside, 10% (v/v) glycerol, 14% (w/v) PEG-8000, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 37944 / Num. obs: 37716 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.1
Reflection shellResolution: 2.8→2.85 Å / Mean I/σ(I) obs: 1.6 / Num. unique all: 1867 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3HVT

3hvt


Resolution: 2.8→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2279111.09 / Data cutoff low absF: 0 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
Details: This structure was refined against data that were sharpened by applying a B-factor correction of -60 using the CCP4 program CAD. These sharpened data are contained in the structure factor file for this entry.
RfactorNum. reflection% reflectionSelection details
Rfree0.312 1995 5.6 %RANDOM
Rwork0.262 ---
all0.267 37944 --
obs0.262 35855 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.312 Å2 / ksol: 0.325981 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-12.79 Å20 Å220.51 Å2
2---8.29 Å20 Å2
3----4.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7759 0 27 0 7786
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.096
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it1.841.5
X-RAY DIFFRACTIONc_mcangle_it3.312
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.572.5
LS refinement shellHighest resolution: 2.8 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork5020 -
Rfree-5.7 %

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