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- PDB-1bqn: TYR 188 LEU HIV-1 RT/HBY 097 -

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Basic information

Entry
Database: PDB / ID: 1bqn
TitleTYR 188 LEU HIV-1 RT/HBY 097
Components(REVERSE TRANSCRIPTASE) x 2
KeywordsNUCLEOTIDYLTRANSFERASE / AIDS / RNA-DIRECTED DNA POLYMERASE / HIV-1 RT/HBY 097 / DRUG-RESISTANT MUTANT
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease 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 / proteolysis / DNA binding / RNA 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 / 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-HBY / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHsiou, Y. / Das, K. / Ding, J. / Arnold, E.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance.
Authors: Hsiou, Y. / Das, K. / Ding, J. / Clark Jr., A.D. / Kleim, J.P. / Rosner, M. / Winkler, I. / Riess, G. / Hughes, S.H. / Arnold, E.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal Structures of 8-Cl and 9-Cl TIBO Complexed with Wild-Type HIV-1 RT and 8-Cl TIBO Complexed with the Tyr181Cys HIV-1 RT Drug-Resistant Mutant
Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Junior, A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Junior, R.H. / Kroeger Smith, M. ...Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Junior, A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Junior, R.H. / Kroeger Smith, M.B. / Michejda, C.J. / Hughes, S.H. / Arnold, E.
#2: Journal: Drug Des.Discovery / Year: 1996
Title: Targeting HIV Reverse Transcriptase for Anti-Aids Drug Design: Structural and Biological Considerations for Chemotherapeutic Strategies
Authors: Arnold, E. / Das, K. / Ding, J. / Yadav, P.N. / Hsiou, Y. / Boyer, P.L. / Hughes, S.H.
#3: Journal: Structure / Year: 1996
Title: Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A Resolution: Implications of Conformational Changes for Polymerization and Inhibition Mechanisms
Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark Junior, A.D. / Hughes, S.H. / Arnold, E.
#4: Journal: Structure / Year: 1995
Title: Structure of HIV-1 Reverse Transcriptase in a Complex with the Non-Nucleoside Inhibitor Alpha-Apa R 95845 at 2.8 A Resolution
Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Junior, A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P. ...Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Junior, A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P.A.J. / Smith Junior, R.H. / Kroeger Koepke, M. / Michejda, C.J. / Hughes, S.H. / Arnold, E.
#5: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors
Authors: Ding, J. / Das, K. / Moereels, H. / Koymans, L. / Andries, K. / Janssen, P.A. / Hughes, S.H. / Arnold, E.
#6: Journal: J.Mol.Biol. / Year: 1994
Title: Locations of Anti-Aids Drug Binding Sites and Resistance Mutations in the Three-Dimensional Structure of HIV-1 Reverse Transcriptase. Implications for Mechanisms of Drug Inhibition and Resistance
Authors: Tantillo, C. / Ding, J. / Jacobo-Molina, A. / Nanni, R.G. / Boyer, P.L. / Hughes, S.H. / Pauwels, R. / Andries, K. / Janssen, P.A. / Arnold, E.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 A Resolution Shows Bent DNA
Authors: Jacobo-Molina, A. / Ding, J. / Nanni, R.G. / Clark Junior, A.D. / Lu, X. / Tantillo, C. / Williams, R.L. / Kamer, G. / Ferris, A.L. / Clark, P. / Hizi, A. / Hughes, S.H. / Arnold, E.
History
DepositionAug 17, 1998Processing site: BNL
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REVERSE TRANSCRIPTASE
B: REVERSE TRANSCRIPTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7393
Polymers114,3982
Non-polymers3401
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-26 kcal/mol
Surface area48770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.800, 69.300, 105.300
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein REVERSE TRANSCRIPTASE / / HIV-1 RT


Mass: 64222.660 Da / Num. of mol.: 1 / Mutation: Y188L, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH10 / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein REVERSE TRANSCRIPTASE / / HIV-1 RT


Mass: 50175.680 Da / Num. of mol.: 1 / Mutation: Y188L, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH10 / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical ChemComp-HBY / (S)-4-ISOPROPOXYCARBONYL-6-METHOXY-3-METHYLTHIOMETHYL-3,4-DIHYDROQUINOXALIN-2(1H)-THIONE / HBY 097


Mass: 340.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N2O3S2

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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: 3.45 Å3/Da / Density % sol: 65 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMinhibitor1drop
320 %(w/v)n-octyl beta-D-glucopyranoside1drop
440 mg/mlenzyme1drop
510 mMTris-HCl1drop
675 mM1dropNaCl
750 mMbis-Tris propane1reservoir
8100 mMammonium sulfate1reservoir
910 %(v/v)glycerol1reservoir
2DMSO1drop
1010 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Mar 1, 1996 / Details: WIGGLERS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 29728 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 79.4 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.14
Reflection shellResolution: 3→3.08 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.7 / % possible all: 97.1
Reflection shell
*PLUS
% possible obs: 97.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TVR

1tvr


Resolution: 3.3→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 10 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.362 1758 6 %RANDOM
Rwork0.245 ---
obs0.245 18523 95.1 %-
Displacement parametersBiso mean: 48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.73 Å0.61 Å
Luzzati d res low-10 Å
Luzzati sigma a0.78 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7816 0 22 0 7838
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.04
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.3→3.44 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.416 93 3.2 %
Rwork0.332 1736 -
obs--85.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.04
LS refinement shell
*PLUS
Rfactor obs: 0.332

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