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- PDB-3tam: Crystal structure of HIV-1 reverse transcriptase (K103N mutant) i... -

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Basic information

Entry
Database: PDB / ID: 3tam
TitleCrystal structure of HIV-1 reverse transcriptase (K103N mutant) in complex with inhibitor M06
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTransferase/transferase Inhibitor / HIV-1 reverse transcriptase / non-nucleoside inhibition / nucleotidyltranferase / K103N / HIV-1 / Transferase-transferase Inhibitor complex
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 / protein processing / Budding and maturation of HIV virion / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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 / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / zinc ion binding / identical protein binding
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 DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / 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-M06 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.51 Å
AuthorsYan, Y.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Design and synthesis of pyridone inhibitors of non-nucleoside reverse transcriptase.
Authors: Gomez, R. / Jolly, S. / Williams, T. / Tucker, T. / Tynebor, R. / Vacca, J. / McGaughey, G. / Lai, M.T. / Felock, P. / Munshi, V. / DeStefano, D. / Touch, S. / Miller, M. / Yan, Y. / ...Authors: Gomez, R. / Jolly, S. / Williams, T. / Tucker, T. / Tynebor, R. / Vacca, J. / McGaughey, G. / Lai, M.T. / Felock, P. / Munshi, V. / DeStefano, D. / Touch, S. / Miller, M. / Yan, Y. / Sanchez, R. / Liang, Y. / Paton, B. / Wan, B.L. / Anthony, N.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Sep 13, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,9883
Polymers116,5972
Non-polymers3921
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-26 kcal/mol
Surface area44240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.910, 153.900, 155.690
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 / Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT


Mass: 64880.238 Da / Num. of mol.: 1 / Fragment: unp residues 590-1147 / Mutation: K103N
Source method: isolated from a genetically manipulated source
Details: p66 RT / Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: HXB2 / Gene: gag-pol, HIV-1 / Production host: Escherichia coli (E. coli)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein p51 RT / REVERSE TRANSCRIPTASE/RIBONUCLEASE H / EXORIBONUCLEASE H / P51 RT


Mass: 51716.340 Da / Num. of mol.: 1 / Fragment: unp residues 588-1027 / Mutation: K103N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: HXB2 / Gene: gag-pol, HIV-1 / Production host: Escherichia coli (E. coli)
References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#3: Chemical ChemComp-M06 / 3-chloro-5-{[4-methyl-2-oxo-1-(2H-pyrazolo[3,4-b]pyridin-3-ylmethyl)-1,2-dihydropyridin-3-yl]oxy}benzonitrile


Mass: 391.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14ClN5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 298 K / 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: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. obs: 42589 / % possible obs: 87.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 63.83 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BUSTER2.9.4refinement
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.9.4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3LP1

3lp1


Resolution: 2.51→16.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.473 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2150 5.08 %RANDOM
Rwork0.193 ---
obs0.196 42363 87.5 %-
Displacement parametersBiso mean: 62.82 Å2
Baniso -1Baniso -2Baniso -3
1-6.1089 Å20 Å20 Å2
2---1.0951 Å20 Å2
3----5.0138 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.51→16.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7837 0 28 362 8227
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018077HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2510977HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2805SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes230HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1097HARMONIC5
X-RAY DIFFRACTIONt_it8077HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion22.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1041SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9193SEMIHARMONIC4
LS refinement shellResolution: 2.51→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3603 54 5.17 %
Rwork0.2576 991 -
all0.2625 1045 -
obs--87.45 %

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