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- PDB-1dtq: CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH ... -

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Entry
Database: PDB / ID: 1dtq
TitleCRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH PETT-1 (PETT131A94)
Components
  • HIV-1 RT A-CHAIN
  • HIV-1 RT B-CHAIN
KeywordsHYDROLASE/TRANSFERASE / HIV-1 reverse transcriptase AIDS / non-nucleoside inhibitor / drug design / HYDROLASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 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 / 2-LTR circle formation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 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 / exoribonuclease H / Assembly Of The HIV Virion / RNA-directed DNA polymerase activity / 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 / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / host cell / viral nucleocapsid / DNA recombination / symbiont-mediated suppression of host gene expression / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / 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 / 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 / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain 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-FPT / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsRen, J. / Diprose, J. / Warren, J. / Esnouf, R.M. / Bird, L.E. / Ikemizu, S. / Slater, M. / Milton, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Phenylethylthiazolylthiourea (PETT) non-nucleoside inhibitors of HIV-1 and HIV-2 reverse transcriptases. Structural and biochemical analyses.
Authors: Ren, J. / Diprose, J. / Warren, J. / Esnouf, R.M. / Bird, L.E. / Ikemizu, S. / Slater, M. / Milton, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K.
#1: Journal: J.Med.Chem. / Year: 1999
Title: Crystallographic analysis of the binding modes of thiazoloisoindolinone non-nucleoside inhibitors to HIV-1 reverse transcriptase and comparison with modeling studies.
Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Stuart, D.I. / Stammers, D.K.
#2: Journal: J.Med.Chem. / Year: 1999
Title: Design of MKC-442 (emivirine) analogues with improved activity against drug-resistant HIV mutants.
Authors: Hopkins, A.L. / Ren, J. / Tanaka, H. / Baba, M. / Okamato, M. / Stuart, D.I. / Stammers, D.K.
#3: Journal: Biochemistry / Year: 1998
Title: Crystal structures of HIV-1 reverse transcriptase in complex with carboxanilide derivatives.
Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Warren, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: 3'-Azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes.
Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Jones, E.Y. / Kirby, I. / Keeling, J. / Ross, C.K. / Larder, B.A. / Stuart, D.I. / Stammers, D.K.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Continuous and discontinuous changes in the unit cell of HIV-1 reverse transcriptase crystals on dehydration.
Authors: Esnouf, R.M. / Ren, J. / Garman, E.F. / Somers, D.O. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (BHAP) U-90152 explain resistance mutations for this nonnucleoside inhibitor.
Authors: Esnouf, R.M. / Ren, J. / Hopkins, A.L. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I.
#7: Journal: J.Med.Chem. / Year: 1996
Title: Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors.
Authors: Hopkins, A.L. / Ren, J. / Esnouf, R.M. / Willcox, B.E. / Jones, E.Y. / Ross, C. / Miyasaka, T. / Walker, R.T. / Tanaka, H. / Stammers, D.K. / Stuart, D.I.
#8: Journal: Structure / Year: 1995
Title: The structure of HIV-1 reverse transcriptase complexed with 9-chloro-TIBO: lessons for inhibitor design.
Authors: Ren, J. / Esnouf, R. / Hopkins, A. / Ross, C. / Jones, Y. / Stammers, D. / Stuart, D.
#9: Journal: Nat.Struct.Biol. / Year: 1995
Title: High resolution structures of HIV-1 RT from four RT-inhibitor complexes.
Authors: Ren, J. / Esnouf, R. / Garman, E. / Somers, D. / Ross, C. / Kirby, I. / Keeling, J. / Darby, G. / Jones, Y. / Stuart, D.
#10: Journal: Nat.Struct.Biol. / Year: 1995
Title: Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors.
Authors: Esnouf, R. / Ren, J. / Ross, C. / Jones, Y. / Stammers, D. / Stuart, D.
#11: Journal: J.Mol.Biol. / Year: 1994
Title: Crystals of HIV-1 reverse transcriptase diffracting to 2.2 A resolution.
Authors: Stammers, D.K. / Somers, D.O. / Ross, C.K. / Kirby, I. / Ray, P.H. / Wilson, J.E. / Norman, M. / Ren, J.S. / Esnouf, R.M. / Garman, E.F.
History
DepositionJan 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Database references / Other
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: HIV-1 RT A-CHAIN
B: HIV-1 RT B-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3393
Polymers115,9942
Non-polymers3451
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-32 kcal/mol
Surface area45080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.1, 115.0, 65.6
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HIV-1 RT A-CHAIN


Mass: 64594.949 Da / Num. of mol.: 1 / Fragment: P66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Bacteria (eubacteria) / References: UniProt: P04585
#2: Protein HIV-1 RT B-CHAIN


Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: P51
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Bacteria (eubacteria) / References: UniProt: P04585
#3: Chemical ChemComp-FPT / N-[[3-FLUORO-4-ETHOXY-PYRID-2-YL]ETHYL]-N'-[5-NITRILOMETHYL-PYRIDYL]-THIOUREA


Mass: 345.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16FN5OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: see reference 11, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Details: Ren, J., (1995) Nat.Struct.Biol., 2, 293.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %PEG34001reservoir
2citrate/phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 25847 / % possible obs: 95.9 % / Observed criterion σ(I): -1.5 / Redundancy: 3.45 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.525 / Num. unique all: 2203 / % possible all: 82.6
Reflection
*PLUS
Num. measured all: 89165
Reflection shell
*PLUS
% possible obs: 82.6 % / Num. unique obs: 2203

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Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Due to the low ratio between the number of reflections and the number of parameters to be refined, positional restraints were applied to all atoms distant from the NNRTI-binding site ...Details: Due to the low ratio between the number of reflections and the number of parameters to be refined, positional restraints were applied to all atoms distant from the NNRTI-binding site (defined as greater than 25 anstrom from the CA atom of residue 188) throughout the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1205 -random
Rwork0.224 ---
obs0.213 24936 95 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7637 0 24 26 7687
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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