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- PDB-5c25: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 5c25
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with 6-((4-((4-cyanophenyl)amino)-1,3,5-triazin-2-yl)amino)-5,7-dimethyl-2-naphthonitrile (JLJ639), a Non-nucleoside Inhibitor
Components(HIV-1 REVERSE TRANSCRIPTASE, ...) x 2
KeywordsTRANSFERASE / HYDROLASE/INHIBITOR / Polymerase / reverse transcriptase / HIV / non-nucleoside inhibitor / HYDROLASE-DNA-INHIBITOR complex / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / 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 / proteolysis / DNA 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. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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. / Ribonuclease H superfamily / 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-639 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.841 Å
AuthorsChan, A.H. / Frey, K.M. / Anderson, K.S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI27690 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI44616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM32136 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49551 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI104334 United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Discovery and crystallography of bicyclic arylaminoazines as potent inhibitors of HIV-1 reverse transcriptase.
Authors: Lee, W.G. / Frey, K.M. / Gallardo-Macias, R. / Spasov, K.A. / Chan, A.H. / Anderson, K.S. / Jorgensen, W.L.
History
DepositionJun 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6376
Polymers114,0292
Non-polymers6084
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-63 kcal/mol
Surface area46640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.554, 72.969, 109.479
Angle α, β, γ (deg.)90.00, 100.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

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HIV-1 REVERSE TRANSCRIPTASE, ... , 2 types, 2 molecules AB

#1: Protein HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT / Pr160Gag-Pol


Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: UNP residues 600-1154 / Mutation: C280S, K172A, K173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT / Pr160Gag-Pol


Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: UNP residues 600-1027 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H

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Non-polymers , 4 types, 31 molecules

#3: Chemical ChemComp-639 / 6-({4-[(4-cyanophenyl)amino]-1,3,5-triazin-2-yl}amino)-5,7- dimethyl-2-naphthonitrile


Mass: 391.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H17N7
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG 8000, 100 mM Ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine, 15 mM HEPES pH 7.0
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 29671 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 49.07 Å2 / Rsym value: 0.146 / Net I/σ(I): 14.61
Reflection shellResolution: 2.84→3.01 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.95 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSMarch 1, 2015data reduction
XDSMarch 1, 2015data scaling
PHASER1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZD1

2zd1


Resolution: 2.841→43.458 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0.74 / Phase error: 29.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 1484 5 %Random selection
Rwork0.2162 ---
obs0.2185 29669 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 2.841→43.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7829 0 41 27 7897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028085
X-RAY DIFFRACTIONf_angle_d0.55210998
X-RAY DIFFRACTIONf_dihedral_angle_d10.7593032
X-RAY DIFFRACTIONf_chiral_restr0.0221191
X-RAY DIFFRACTIONf_plane_restr0.0031380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8414-2.93310.40551250.3372372X-RAY DIFFRACTION93
2.9331-3.03790.41531350.31332568X-RAY DIFFRACTION99
3.0379-3.15950.31091340.30352551X-RAY DIFFRACTION99
3.1595-3.30320.37931350.29552572X-RAY DIFFRACTION99
3.3032-3.47730.31071340.25232531X-RAY DIFFRACTION99
3.4773-3.69510.26341350.22712570X-RAY DIFFRACTION99
3.6951-3.98020.21491350.19632568X-RAY DIFFRACTION100
3.9802-4.38040.2261370.1762590X-RAY DIFFRACTION100
4.3804-5.01350.19341360.17262590X-RAY DIFFRACTION100
5.0135-6.31330.26431370.19432605X-RAY DIFFRACTION100
6.3133-43.46270.21871410.17462668X-RAY DIFFRACTION100

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