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- PDB-9wa5: Crystal structure of an inactive form of NS2B-NS3 Protease -

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Basic information

Entry
Database: PDB / ID: 9wa5
TitleCrystal structure of an inactive form of NS2B-NS3 Protease
ComponentsSerine protease subunit NS2B,Serine protease NS3
KeywordsVIRAL PROTEIN / Zika virus / viral protease / NS2B-NS3
Function / homology
Function and homology information


symbiont-mediated suppression of host interferon-mediated signaling pathway / flavivirin / 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 JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host interferon-mediated signaling pathway / flavivirin / 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 JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell cytoplasm / protein-macromolecule adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / serine-type endopeptidase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / 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 / GTP binding / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis 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 / Immunoglobulin E-set / helicase superfamily c-terminal domain / 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNgo, K.H. / Liew, C.W. / Luo, D. / Kang, C.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19-AI171954 United States
CitationJournal: J.Struct.Biol. / Year: 2026
Title: An inactive Zika NS2B-NS3pro protease construct for investigating allosteric inhibitors.
Authors: Ngo, K.H. / Lattmann, S. / Anindita, P.D. / Liew, C.W. / Harris, R.S. / Luo, D. / Kang, C.
History
DepositionAug 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease subunit NS2B,Serine protease NS3
B: Serine protease subunit NS2B,Serine protease NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2466
Polymers45,0732
Non-polymers1734
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-26 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.221, 55.221, 251.523
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Serine protease subunit NS2B,Serine protease NS3 / Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B / Flavivirin protease NS3 ...Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 22536.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: g18Zipro, inactive form of NS2B-NS3 Protease / Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.03M Magnesium chloride hexahydrate, 0.03M Calcium chloride dihydrate, 0.1M Buffer Tris (base)/BICINE 8.5, 20% v/v Ethylene glycol, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.4→41.492 Å / Num. obs: 16175 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 40.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.442 Å / Num. unique obs: 19997 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→41.49 Å / SU ML: 0.361 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9465
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2422 1617 10 %
Rwork0.2275 14545 -
obs0.2289 16162 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.95 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 10 75 2551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972523
X-RAY DIFFRACTIONf_angle_d1.26953416
X-RAY DIFFRACTIONf_chiral_restr0.0762373
X-RAY DIFFRACTIONf_plane_restr0.0421438
X-RAY DIFFRACTIONf_dihedral_angle_d18.2451908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.36271270.341159X-RAY DIFFRACTION99.92
2.47-2.550.4021310.32951173X-RAY DIFFRACTION100
2.55-2.640.35451330.31251194X-RAY DIFFRACTION99.85
2.64-2.750.28311320.28731181X-RAY DIFFRACTION99.85
2.75-2.870.28391310.26341183X-RAY DIFFRACTION99.85
2.87-3.020.32121320.26521190X-RAY DIFFRACTION99.85
3.02-3.210.24271330.25561188X-RAY DIFFRACTION99.92
3.21-3.460.29551350.24121218X-RAY DIFFRACTION99.93
3.46-3.810.23471330.21011204X-RAY DIFFRACTION100
3.81-4.360.18981380.18461236X-RAY DIFFRACTION100
4.36-5.490.15831400.16951259X-RAY DIFFRACTION99.93
5.49-41.490.22471520.21271360X-RAY DIFFRACTION99.87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0272097184-1.56566959086-1.471133510457.343953100243.646016960042.895814610670.401777562985-0.1087584405480.31367968699-0.7280533410730.405208811-1.55900090737-0.292751892871.1576362904-0.3726435012140.4836410406410.0710212159630.06307223128440.722140226855-0.03558961940310.524141754712-17.04165108083.45293165421-57.059017971
23.684513542050.535900638744-0.7005696453385.636012497543.433481249145.884011598280.00856500059476-0.02874297085340.0973932021691-0.1981287357980.200744863761-0.1933147656260.1808495842620.228275033226-0.1800513672610.3838176287510.04842798108950.01420517410340.502017397714-0.0536605103940.249619350436-24.73288641367.20458954561-48.5487510911
34.65620800201-3.40539823566-0.7626433189915.52756028742.481920388373.977312179330.2006361244950.141134298295-0.0556870554767-0.0958804423039-0.5905625563520.407821686523-0.0446247723537-0.589563837660.3761105543680.582652637210.0117908865305-0.03693293557530.602507004065-0.05519458114070.294728024963-31.70705964862.89804891198-54.5096300709
43.05387106444-1.76508961842-1.808416431014.94474267745-0.8176935206165.662005923110.003423892062980.16481861809-0.1214687610290.009982611570190.2784499196580.07593593724510.8098331952060.677412258655-0.391624990890.6597050972640.152069375452-0.07417837586610.555091622647-0.09985632288030.300544569652-20.2481969328-8.31445201786-51.1636374398
55.29793867251-2.79583358956-0.6632579736273.56145166747-1.415420272251.963953846180.3807514191030.665665520493-0.918556297981-0.5280352380330.01242022128230.5711289692281.21155413261-0.538658323184-0.2234139113830.9486546709510.00912494218819-0.1240568754220.718669102916-0.1898481189050.322604561074-28.2048588475-9.96135320825-61.2755130828
64.077944654033.25418484191.071510079366.93717586732.732788243052.572087165010.603813531088-0.217791055195-1.191808212030.6882162862570.00235549131023-0.6462187710361.146394127420.21732585951-0.1435171188980.615338374780.0005458502858020.05277589554230.4557246051530.08403117004240.339395274923-25.699669408-3.19704345917-22.4645926314
73.648766501250.0437661499527-0.03805294001182.948097741731.074708352164.398095239630.06807825006490.122527480845-0.1553757303120.000692195094165-0.1581978453090.2997963141460.403274732013-0.5331140916430.1236719610430.300910476591-0.06086909864480.001052534527010.483198006297-0.02918995811920.206884369218-32.86744206543.5945930353-27.7300730861
83.852269532990.354324609130.7010615933994.680770289391.43110483594.532776408370.0617540001004-0.1927965240920.169743224585-0.40589442366-0.0328401515780.02308622390240.002970218410560.1199337283840.006682773971310.2966701245520.00954109971072-0.008403662238280.4820760022310.01109639175610.204199908052-19.86564064549.68801677496-24.4999181062
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -26 through 20 )AA-26 - 201 - 22
22chain 'A' and (resid 21 through 53 )AA21 - 5323 - 55
33chain 'A' and (resid 54 through 94 )AA54 - 9456 - 96
44chain 'A' and (resid 95 through 137 )AA95 - 13797 - 139
55chain 'A' and (resid 138 through 163 )AA138 - 163140 - 165
66chain 'B' and (resid -27 through 20 )BB-27 - 201 - 23
77chain 'B' and (resid 21 through 94 )BB21 - 9424 - 97
88chain 'B' and (resid 95 through 157 )BB95 - 15798 - 160

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