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- PDB-8kdz: DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-Adenosyl-L-homocysteine... -

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Basic information

Entry
Database: PDB / ID: 8kdz
TitleDENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-Adenosyl-L-homocysteine and Caffeic acid phenethyl ester
Componentsmethyltransferase
KeywordsVIRAL PROTEIN / Inhibitor / Methyltransferase / Dengue 3 / Antiviral
Function / homology
Function and homology information


host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / serine-type endopeptidase activity / symbiont-mediated activation of host autophagy / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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 / 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
Similarity search - Domain/homology
Chem-QAP / S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein
Similarity search - Component
Biological speciesdengue virus type 3
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBhutkar, M. / Kumar, A. / Tomar, S. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical Research India
CitationJournal: Febs Lett. / Year: 2025
Title: Structure-based identification of herbacetin and caffeic acid phenethyl ester as inhibitors of S-adenosylmethionine-dependent viral methyltransferase.
Authors: Bhutkar, M. / Kumar, A. / Rani, R. / Singh, V. / Saha, A. / Pathak, A. / Kothiala, A. / Mahajan, S. / Waghmode, B. / Verma, S. / Kumar, R. / Mudgal, R. / Sircar, D. / Kumar, P. / Tomar, S.
History
DepositionAug 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: methyltransferase
B: methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5536
Polymers64,2162
Non-polymers1,3374
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.648, 60.722, 184.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 7 - 262 / Label seq-ID: 26 - 281

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein methyltransferase / Genome polyprotein


Mass: 32107.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) dengue virus type 3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C1KBQ3
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-QAP / 2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate


Mass: 284.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.4122386 Å3/Da / Density % sol: 49.041695 % / Description: Square Shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 8000 100 mM Tris 200 mM NaCl 20 mM Trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→23.056 Å / Num. obs: 108535 / % possible obs: 98.6 % / Redundancy: 6 % / Rrim(I) all: 0.188 / Net I/σ(I): 7.3
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 18527 / Rrim(I) all: 0.421 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R8R

4r8r


Resolution: 2.6→23.056 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.852 / SU B: 14.568 / SU ML: 0.305 / Cross valid method: FREE R-VALUE / ESU R: 2.222 / ESU R Free: 0.358 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2727 924 5.004 %
Rwork0.231 17543 -
all0.233 --
obs-108535 99.328 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.803 Å2
Baniso -1Baniso -2Baniso -3
1--2.711 Å2-0 Å2-0 Å2
2---2.122 Å20 Å2
3---4.833 Å2
Refinement stepCycle: LAST / Resolution: 2.6→23.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 94 124 4304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124274
X-RAY DIFFRACTIONr_ext_dist_refined_d0.3370.168107
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.6525764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51620.545220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25915784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6611538
X-RAY DIFFRACTIONr_chiral_restr0.0970.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023202
X-RAY DIFFRACTIONr_nbd_refined0.2140.21941
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2150
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.280.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2650.26
X-RAY DIFFRACTIONr_mcbond_it1.5012.7422052
X-RAY DIFFRACTIONr_mcangle_it2.4894.1092558
X-RAY DIFFRACTIONr_scbond_it2.1363.032222
X-RAY DIFFRACTIONr_scangle_it3.324.4383206
X-RAY DIFFRACTIONr_lrange_it7.097101.26470623
X-RAY DIFFRACTIONr_ncsr_local_group_10.1170.058368
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.117360.05008
12BX-RAY DIFFRACTIONLocal ncs0.117360.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6680.309570.3061276X-RAY DIFFRACTION98.8139
2.668-2.7410.405750.2981243X-RAY DIFFRACTION100
2.741-2.820.331600.2941198X-RAY DIFFRACTION99.9206
2.82-2.9070.333540.2651203X-RAY DIFFRACTION99.9205
2.907-3.0020.277780.2451110X-RAY DIFFRACTION100
3.002-3.1070.316560.2481106X-RAY DIFFRACTION100
3.107-3.2250.307570.261101X-RAY DIFFRACTION99.9137
3.225-3.3560.294390.2521031X-RAY DIFFRACTION99.8134
3.356-3.5060.287500.24988X-RAY DIFFRACTION99.8077
3.506-3.6770.243480.228957X-RAY DIFFRACTION99.7024
3.677-3.8750.327680.224902X-RAY DIFFRACTION99.897
3.875-4.110.176450.208851X-RAY DIFFRACTION99.4451
4.11-4.3940.231390.197823X-RAY DIFFRACTION98.74
4.394-4.7460.243330.187754X-RAY DIFFRACTION98.7453
4.746-5.1980.226450.188696X-RAY DIFFRACTION98.9319
5.198-5.8120.285410.224635X-RAY DIFFRACTION99.8523
5.812-6.7090.251230.226588X-RAY DIFFRACTION99.1883
6.709-8.2150.194230.194481X-RAY DIFFRACTION98.8235
8-100.271130.232205X-RAY DIFFRACTION83.5249
8.215-11.6060.19200.151395X-RAY DIFFRACTION97.8774

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