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- PDB-7kwu: Crystal Structure of HIV-1 RT in Complex with 16c (K07-15) -

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Basic information

Entry
Database: PDB / ID: 7kwu
TitleCrystal Structure of HIV-1 RT in Complex with 16c (K07-15)
Components(Reverse transcriptase ...) x 2
KeywordsTRANSFERASE/INHIBITOR / Human immunodeficiency virus 1 / non nucleotide-reverse transcriptase inhibitor / TRANSFERASE / TRANSFERASE-INHIBITOR complex
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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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. / 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 / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-K7F / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsRuiz, F.X. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)MERIT Award R37 AI027690 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: 2,4,5-Trisubstituted Pyrimidines as Potent HIV-1 NNRTIs: Rational Design, Synthesis, Activity Evaluation, and Crystallographic Studies.
Authors: Kang, D. / Ruiz, F.X. / Sun, Y. / Feng, D. / Jing, L. / Wang, Z. / Zhang, T. / Gao, S. / Sun, L. / De Clercq, E. / Pannecouque, C. / Arnold, E. / Zhan, P. / Liu, X.
History
DepositionDec 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Reverse transcriptase p66
B: Reverse transcriptase p51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,53015
Polymers114,0862
Non-polymers1,44513
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: 1 biological assembliy in the asymmetric unit: A,B
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-106 kcal/mol
Surface area46480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.379, 72.622, 109.723
Angle α, β, γ (deg.)90.000, 100.205, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Reverse transcriptase ... , 2 types, 2 molecules AB

#1: Protein Reverse transcriptase p66


Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein Reverse transcriptase p51


Mass: 50096.539 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366

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Non-polymers , 5 types, 709 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K7F / 4-[(4-{[4-(4-cyano-2,6-dimethylphenoxy)-5-(pyridin-4-yl)pyrimidin-2-yl]amino}piperidin-1-yl)methyl]benzamide


Mass: 533.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H31N7O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 696 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10%(v/v) PEG 8000, 4%(v/v) PEG 400, 100 mM MES pH 6.3-6.6, 10 mM spermine, 15 mM MgSO4, 100 mM ammonium sulfate, and 5 mM tris(2-carboxyethyl)phosphine
PH range: 6.3-6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03326 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03326 Å / Relative weight: 1
ReflectionResolution: 2.02→29.54 Å / Num. obs: 83044 / % possible obs: 100 % / Redundancy: 17.8 % / Biso Wilson estimate: 31.67 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.503 / Rpim(I) all: 0.124 / Rrim(I) all: 0.518 / Net I/σ(I): 9.6
Reflection shellResolution: 2.02→2.06 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4512 / CC1/2: 0.383 / Rpim(I) all: 3.396 / Rrim(I) all: 12.606 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q


Resolution: 2.02→29.54 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2589 4102 4.94 %
Rwork0.2115 78940 -
obs0.2139 83042 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.41 Å2
Refinement stepCycle: LAST / Resolution: 2.02→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7930 0 91 696 8717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00348356
X-RAY DIFFRACTIONf_angle_d0.666811374
X-RAY DIFFRACTIONf_chiral_restr0.04761220
X-RAY DIFFRACTIONf_plane_restr0.00351464
X-RAY DIFFRACTIONf_dihedral_angle_d20.9823177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.040.34611400.32232677X-RAY DIFFRACTION100
2.04-2.070.38671290.30922744X-RAY DIFFRACTION100
2.07-2.090.34791310.30822696X-RAY DIFFRACTION100
2.09-2.120.34661270.30122752X-RAY DIFFRACTION100
2.12-2.150.30781490.29212653X-RAY DIFFRACTION100
2.15-2.180.35271420.28072730X-RAY DIFFRACTION100
2.18-2.210.30131350.28072684X-RAY DIFFRACTION100
2.21-2.250.30881450.27792712X-RAY DIFFRACTION100
2.25-2.290.33251220.27862733X-RAY DIFFRACTION100
2.29-2.330.33981420.26732690X-RAY DIFFRACTION100
2.33-2.370.30911360.2562743X-RAY DIFFRACTION100
2.37-2.410.31141420.26142718X-RAY DIFFRACTION100
2.41-2.460.30681330.25232690X-RAY DIFFRACTION100
2.46-2.520.32181370.2412737X-RAY DIFFRACTION100
2.52-2.570.31811630.23492688X-RAY DIFFRACTION100
2.57-2.640.2711390.2292707X-RAY DIFFRACTION100
2.64-2.710.26961360.23372733X-RAY DIFFRACTION100
2.71-2.790.26861470.22832729X-RAY DIFFRACTION100
2.79-2.880.28581250.22172731X-RAY DIFFRACTION100
2.88-2.980.26331400.21922720X-RAY DIFFRACTION100
2.98-3.10.2591640.21742683X-RAY DIFFRACTION100
3.1-3.240.27931550.20562726X-RAY DIFFRACTION100
3.24-3.410.27811290.20432741X-RAY DIFFRACTION100
3.41-3.630.25581480.18822723X-RAY DIFFRACTION100
3.63-3.910.22681390.1782746X-RAY DIFFRACTION100
3.91-4.30.21341580.16232720X-RAY DIFFRACTION100
4.3-4.920.20521600.1622726X-RAY DIFFRACTION99.97
4.92-6.190.22211550.18192755X-RAY DIFFRACTION100
6.19-29.540.20361340.1832853X-RAY DIFFRACTION99.97

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