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- PDB-5hmy: Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 15 -

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Basic information

Entry
Database: PDB / ID: 5hmy
TitleDengue serotype 3 RNA-dependent RNA polymerase bound to compound 15
ComponentsRNA-directed RNA polymerase NS5
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor Complex Polymerase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / mRNA (guanine-N7)-methyltransferase ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / viral RNA genome replication / serine-type endopeptidase activity / DNA clamp loader activity / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / : / viral envelope / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B ...Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LNY / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNoble, C.G.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery of Potent Non-Nucleoside Inhibitors of Dengue Viral RNA-Dependent RNA Polymerase from a Fragment Hit Using Structure-Based Drug Design.
Authors: Yokokawa, F. / Nilar, S. / Noble, C.G. / Lim, S.P. / Rao, R. / Tania, S. / Wang, G. / Lee, G. / Hunziker, J. / Karuna, R. / Manjunatha, U. / Shi, P.Y. / Smith, P.W.
History
DepositionJan 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0864
Polymers73,6251
Non-polymers4613
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25810 Å2
Unit cell
Length a, b, c (Å)160.880, 177.110, 58.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1158-

HOH

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Components

#1: Protein RNA-directed RNA polymerase NS5


Mass: 73624.867 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2762-3390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6DLV0, UniProt: Q6YMS4*PLUS, RNA-directed RNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-LNY / 2,2'-(5-(5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl)-1,3-phenylene)diacetic acid


Mass: 330.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsresidue 374 GLU is a naturally occurred mutation in the viral sequence.

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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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M TRIS, 25% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→119.085 Å / Num. obs: 48496 / % possible obs: 99.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 30.53 Å2 / Rsym value: 0.086 / Net I/av σ(I): 8.263 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.213.70.481.5198.7
2.21-2.353.60.3362.2198.6
2.35-2.513.60.2592.9199.2
2.51-2.714.10.1973.8199.8
2.71-2.974.20.1256199.9
2.97-3.3240.0779.7199.3
3.32-3.833.90.04615.6199.6
3.83-4.74.20.03818.61100
4.7-6.643.70.04116.5199.3
6.64-47.0833.60.03219.4199.1

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
BUSTER2.11.5refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
BUSTER-TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HHJ

4hhj


Resolution: 2.1→21.17 Å / Cor.coef. Fo:Fc: 0.9308 / Cor.coef. Fo:Fc free: 0.9168 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.171 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 2451 5.06 %RANDOM
Rwork0.1837 ---
obs0.1852 48425 99.09 %-
Displacement parametersBiso max: 136.34 Å2 / Biso mean: 38.27 Å2 / Biso min: 12.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.9883 Å20 Å20 Å2
2---11.1877 Å20 Å2
3---7.1993 Å2
Refine analyzeLuzzati coordinate error obs: 0.236 Å
Refinement stepCycle: final / Resolution: 2.1→21.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 25 323 5162
Biso mean--27.59 40.35 -
Num. residues----591
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1772SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes718HARMONIC5
X-RAY DIFFRACTIONt_it4988HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion627SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5909SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4988HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6759HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion18.06
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2257 161 4.57 %
Rwork0.2148 3363 -
all0.2153 3524 -
obs--99.09 %

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