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- PDB-8vq2: HSV1 polymerase ternary complex with dsDNA and compound 44 -

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Basic information

Entry
Database: PDB / ID: 8vq2
TitleHSV1 polymerase ternary complex with dsDNA and compound 44
Components
  • DNA (5'-D(P*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
  • DNA (5'-D(P*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*T)-3')
  • DNA polymerase
KeywordsTRANSFERASE / Herpesvirus Polymerase Complex Inhibitor
Function / homology
Function and homology information


viral DNA genome replication / RNA-DNA hybrid ribonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / host cell nucleus / DNA binding
Similarity search - Function
DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family ...DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 (Herpes simplex virus type 1)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.829 Å
AuthorsHayes, R.P. / Heo, M.R. / Plotkin, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Discovery of Broad-Spectrum Herpes Antiviral Oxazolidinone Amide Derivatives and Their Structure-Activity Relationships.
Authors: Plotkin, M.A. / Labroli, M. / Schubert, J. / Shaw, A. / Schlegel, K.S. / Berger, R. / Cooke, A.J. / Hayes, R.P. / Armacost, K.A. / Kinek, K. / Krosky, P. / Burlein, C. / Meng, S. / DiNunzio, ...Authors: Plotkin, M.A. / Labroli, M. / Schubert, J. / Shaw, A. / Schlegel, K.S. / Berger, R. / Cooke, A.J. / Hayes, R.P. / Armacost, K.A. / Kinek, K. / Krosky, P. / Burlein, C. / Meng, S. / DiNunzio, E. / Murray, E.M. / Agrawal, S. / Madeira, M. / Flattery, A. / Yao, H. / Leithead, A. / Rose 2nd, W.A. / Cox, C. / Tellers, D.M. / McKenna, P.M. / Raheem, I.
History
DepositionJan 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
C: DNA (5'-D(P*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*T)-3')
D: DNA (5'-D(P*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
B: DNA polymerase
E: DNA (5'-D(P*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*T)-3')
F: DNA (5'-D(P*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,2668
Polymers276,4276
Non-polymers8392
Water00
1
A: DNA polymerase
C: DNA (5'-D(P*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*T)-3')
D: DNA (5'-D(P*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
hetero molecules


  • defined by author&software
  • 139 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)138,6334
Polymers138,2143
Non-polymers4191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-34 kcal/mol
Surface area47390 Å2
MethodPISA
2
B: DNA polymerase
E: DNA (5'-D(P*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*T)-3')
F: DNA (5'-D(P*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
hetero molecules


  • defined by author&software
  • 139 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)138,6334
Polymers138,2143
Non-polymers4191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-25 kcal/mol
Surface area48030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.628, 180.628, 231.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein DNA polymerase


Mass: 129636.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I7GY94, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*T)-3')


Mass: 4754.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')


Mass: 3822.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-A1AC6 / 2-(4-bromophenyl)-N-(3-methoxy-4-{[(4S)-2-oxo-1,3-oxazolidin-4-yl]methyl}phenyl)acetamide


Mass: 419.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19BrN2O4 / Feature type: SUBJECT OF INVESTIGATION
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: 6.84 Å3/Da / Density % sol: 82.02 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate pH 6.7, 0.6 M succinic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.91936 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91936 Å / Relative weight: 1
ReflectionResolution: 3.829→231.875 Å / Num. obs: 70570 / % possible obs: 98.8 % / Redundancy: 13.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.082 / Net I/σ(I): 11.1
Reflection shellResolution: 3.829→3.895 Å / Rmerge(I) obs: 1.337 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3109 / CC1/2: 0.717 / Rpim(I) all: 0.524 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.829→43.809 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 3408 4.84 %
Rwork0.209 --
obs0.2099 70430 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.829→43.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15917 1130 52 0 17099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417626
X-RAY DIFFRACTIONf_angle_d0.6624224
X-RAY DIFFRACTIONf_dihedral_angle_d17.24610201
X-RAY DIFFRACTIONf_chiral_restr0.0432723
X-RAY DIFFRACTIONf_plane_restr0.0052981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.829-3.88350.31161470.29562822X-RAY DIFFRACTION100
3.8835-3.94140.3172900.29461981X-RAY DIFFRACTION70
3.9414-4.0030.27631350.27432848X-RAY DIFFRACTION100
4.003-4.06850.29411730.27222762X-RAY DIFFRACTION100
4.0685-4.13860.28931220.25662838X-RAY DIFFRACTION100
4.1386-4.21380.3111370.25052873X-RAY DIFFRACTION100
4.2138-4.29480.23341320.23892804X-RAY DIFFRACTION100
4.2948-4.38240.2581250.21872858X-RAY DIFFRACTION100
4.3824-4.47760.25821340.21592820X-RAY DIFFRACTION100
4.4776-4.58170.22841590.21762782X-RAY DIFFRACTION100
4.5817-4.69610.19221240.20832872X-RAY DIFFRACTION100
4.6961-4.82290.2471440.1952825X-RAY DIFFRACTION100
4.8229-4.96470.24221540.19562812X-RAY DIFFRACTION100
4.9647-5.12470.20871490.19952833X-RAY DIFFRACTION100
5.1247-5.30750.25081660.21182811X-RAY DIFFRACTION100
5.3075-5.51970.2331590.21292795X-RAY DIFFRACTION100
5.5197-5.77030.23791490.21282824X-RAY DIFFRACTION100
5.7703-6.07380.24081450.21772821X-RAY DIFFRACTION100
6.0738-6.45320.23011410.2192857X-RAY DIFFRACTION100
6.4532-6.94970.22191700.22322810X-RAY DIFFRACTION100
6.9497-7.64570.1881180.1912866X-RAY DIFFRACTION100
7.6457-8.74450.16651640.17612810X-RAY DIFFRACTION100
8.7445-10.98830.1581300.15182881X-RAY DIFFRACTION100
10.9883-43.8090.23131410.2022817X-RAY DIFFRACTION97

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