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- PDB-3dya: HIV-1 RT with non-nucleoside inhibitor annulated Pyrazole 1 -

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Basic information

Entry
Database: PDB / ID: 3dya
TitleHIV-1 RT with non-nucleoside inhibitor annulated Pyrazole 1
Components
  • REVERSE TRANSCRIPTASE/RIBONUCLEASE H
  • p51 RT
KeywordsTRANSFERASE / PR160GAG-POL / REVERSE TRANSCRIPTASE/RIBONUCLEASE H / P66 RT / P51 RT
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-PZL / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHarris, S.F. / Villasenor, A.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Design of annulated pyrazoles as inhibitors of HIV-1 reverse transcriptase
Authors: Sweeney, Z.K. / Harris, S.F. / Arora, S.F. / Javanbakht, H. / Li, Y. / Fretland, J. / Davidson, J.P. / Billedeau, J.R. / Gleason, S.K. / Hirschfeld, D. / Kennedy-Smith, J.J. / Mirzadegan, T. ...Authors: Sweeney, Z.K. / Harris, S.F. / Arora, S.F. / Javanbakht, H. / Li, Y. / Fretland, J. / Davidson, J.P. / Billedeau, J.R. / Gleason, S.K. / Hirschfeld, D. / Kennedy-Smith, J.J. / Mirzadegan, T. / Roetz, R. / Smith, M. / Sperry, S. / Suh, J.M. / Wu, J. / Tsing, S. / Villasenor, A.G. / Paul, A. / Su, G. / Heilek, G. / Hang, J.Q. / Zhou, A.S. / Jernelius, J.A. / Zhang, F.J. / Klumpp, K.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)116,5683
Polymers116,1092
Non-polymers4591
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-29 kcal/mol
Surface area44320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.662, 153.669, 155.795
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 / REVERSE TRANSCRIPTASE/RIBONUCLEASE H / P66 RT / P51 RT


Mass: 64710.121 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 588-1148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: HXB2 ISOLATE / Gene: gag-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 / REVERSE TRANSCRIPTASE/RIBONUCLEASE H / P66 RT / P51 RT


Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 588-1027
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#3: Chemical ChemComp-PZL / 3-[6-bromo-2-fluoro-3-(1H-pyrazolo[3,4-c]pyridazin-3-ylmethyl)phenoxy]-5-chlorobenzonitrile


Mass: 458.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H10BrClFN5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 59.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1.15 M SODIUM MALONATE, 50 mM POTASSIUM PHOSPHATE PH 7.2, 5% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97839 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97839 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 62828 / Num. obs: 60666 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 64.7 Å2 / Rsym value: 0.071
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.15 / Num. unique all: 3061 / Rsym value: 0.669 / % possible all: 47.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.98 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.206 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 3093 5.1 %RANDOM
Rwork0.21832 ---
obs0.22076 57573 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.177 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7822 0 28 311 8161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228065
X-RAY DIFFRACTIONr_bond_other_d0.0010.025584
X-RAY DIFFRACTIONr_angle_refined_deg1.321.96310964
X-RAY DIFFRACTIONr_angle_other_deg0.878313708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00525.222360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.313151460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8591529
X-RAY DIFFRACTIONr_chiral_restr0.0780.21187
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021496
X-RAY DIFFRACTIONr_nbd_refined0.20.21673
X-RAY DIFFRACTIONr_nbd_other0.1880.25537
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23756
X-RAY DIFFRACTIONr_nbtor_other0.0880.24270
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2317
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.27
X-RAY DIFFRACTIONr_mcbond_it1.031.56203
X-RAY DIFFRACTIONr_mcbond_other0.1171.51899
X-RAY DIFFRACTIONr_mcangle_it1.16927812
X-RAY DIFFRACTIONr_scbond_it1.51834021
X-RAY DIFFRACTIONr_scangle_it2.2794.53152
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 175 -
Rwork0.297 3125 -
obs--71.72 %

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