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- PDB-3di6: HIV-1 RT with pyridazinone non-nucleoside inhibitor -

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Basic information

Entry
Database: PDB / ID: 3di6
TitleHIV-1 RT with pyridazinone non-nucleoside inhibitor
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE / HIV / RT / REVERSE TRANSCRIPTASE / TRANSFERASE RNA-DIRECTED DNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / AIDS / Cytoplasm / Hydrolase / Viral nucleoprotein
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 / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / 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 / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / 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-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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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-PDZ / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHarris, S.F. / Villasenor, A. / Dunten, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Discovery and optimization of pyridazinone non-nucleoside inhibitors of HIV-1 reverse transcriptase.
Authors: Sweeney, Z.K. / Dunn, J.P. / Li, Y. / Heilek, G. / Dunten, P. / Elworthy, T.R. / Han, X. / Harris, S.F. / Hirschfeld, D.R. / Hogg, J.H. / Huber, W. / Kaiser, A.C. / Kertesz, D.J. / Kim, W. / ...Authors: Sweeney, Z.K. / Dunn, J.P. / Li, Y. / Heilek, G. / Dunten, P. / Elworthy, T.R. / Han, X. / Harris, S.F. / Hirschfeld, D.R. / Hogg, J.H. / Huber, W. / Kaiser, A.C. / Kertesz, D.J. / Kim, W. / Mirzadegan, T. / Roepel, M.G. / Saito, Y.D. / Silva, T.M. / Swallow, S. / Tracy, J.L. / Villasenor, A. / Vora, H. / Zhou, A.S. / Klumpp, K.
History
DepositionJun 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 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

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)116,4403
Polymers116,1092
Non-polymers3311
Water1,74797
1
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)232,8806
Polymers232,2184
Non-polymers6612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area16350 Å2
ΔGint-75 kcal/mol
Surface area82940 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-25 kcal/mol
Surface area44240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.046, 153.510, 154.551
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 / p66 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.) Human immunodeficiency virus type 1 (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


Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: UNP residues 588-1027
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (HXB2 isolate)
Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04585
#3: Chemical ChemComp-PDZ / 6-(4-chloro-2-fluoro-3-phenoxybenzyl)pyridazin-3(2H)-one


Mass: 330.741 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12ClFN2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1.15 M sodium malonate, 50 mM potassium phosphate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976067 Å
DetectorDetector: CCD / Date: Aug 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976067 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 40591 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rsym value: 0.0307 / Net I/σ(I): 45
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 8.6 / Num. unique all: 4012 / Rsym value: 0.186 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→46.88 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26537 2064 5.1 %RANDOM
Rwork0.21721 ---
all0.21969 40591 --
obs-38450 99.6 %-
Displacement parametersBiso mean: 43.462 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---1.49 Å20 Å2
3---2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.65→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7788 0 23 97 7908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.068
X-RAY DIFFRACTIONr_angle_other_deg0.784
X-RAY DIFFRACTIONr_chiral_restr0.062
LS refinement shellResolution: 2.65→2.719 Å
RfactorNum. reflection% reflection
Rfree0.373 139 -
Rwork0.3 --
obs-2800 98.8 %

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