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- PDB-5eqs: Crystal structure of a genotype 1a/3a chimeric HCV NS3/4A proteas... -

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Basic information

Entry
Database: PDB / ID: 5eqs
TitleCrystal structure of a genotype 1a/3a chimeric HCV NS3/4A protease in complex with Asunaprevir
ComponentsNS3 protease
KeywordsHYDROLASE/HYDROLASE Inhibitor / Asunaprevir / drug resistance / HCV protease inhibitor / Genotype 3 / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


transformation of host cell by virus / host cell membrane / serine-type peptidase activity / virion component / symbiont entry into host cell / virion attachment to host cell / proteolysis / membrane / metal ion binding
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepacivirus/Pegivirus NS3 protease domain profile. / Hepatitis C virus NS3 protease / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-2R9 / NS3 protease / NS3 protease
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.839 Å
AuthorsSoumana, D. / Yilmaz, N.K. / Ali, A. / Prachanronarong, K.L. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI085051 United States
Citation
Journal: J.Am.Chem.Soc. / Year: 2016
Title: Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease.
Authors: Soumana, D.I. / Kurt Yilmaz, N. / Ali, A. / Prachanronarong, K.L. / Schiffer, C.A.
#1: Journal: ACS Chem. Biol. / Year: 2014
Title: Structural analysis of asunaprevir resistance in HCV NS3/4A protease.
Authors: Soumana, D.I. / Ali, A. / Schiffer, C.A.
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

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Assembly

Deposited unit
A: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1173
Polymers20,3031
Non-polymers8142
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.115, 60.334, 79.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NS3 protease


Mass: 20302.951 Da / Num. of mol.: 1 / Mutation: D168Q, I132L, R123T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Plasmid: pET28-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: C1KIK8, UniProt: A0A0B4WYC6*PLUS
#2: Chemical ChemComp-2R9 / N-(tert-butoxycarbonyl)-3-methyl-L-valyl-(4R)-4-[(7-chloro-4-methoxyisoquinolin-1-yl)oxy]-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-L-prolinamide / Asunaprevir


Mass: 748.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H46ClN5O9S / Comment: inhibitor*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 to 26% PEG-3350, 0.1 M sodium MES buffer at pH 6.5, and 4% ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.839→26.549 Å / Num. all: 15651 / Num. obs: 15651 / % possible obs: 92 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.41 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.106 / Rsym value: 0.094 / Net I/av σ(I): 6.493 / Net I/σ(I): 10.2 / Num. measured all: 69630
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.839-1.892.10.4461.815247240.3670.446259.1
1.89-1.942.40.3652.120208510.2710.3652.672
1.94-1.992.80.2822.726849750.1870.2823.583.8
1.99-2.063.40.2423.2347910300.1430.2424.489.6
2.06-2.124.40.2373.344279960.1190.2375.593
2.12-2.24.60.1953.9471910290.0970.1956.495.3
2.2-2.284.60.1654.6463910060.0830.1657.497.2
2.28-2.374.60.1544.945339810.0780.1547.798.7
2.37-2.484.70.1435.245169570.0710.1438.499.4
2.48-2.64.90.1345.545029190.0660.1349.499.7
2.6-2.7450.1176.343628740.0580.11710.499.8
2.74-2.915.20.0927.542748240.0440.09213.299.9
2.91-3.115.20.0848.541087830.040.08414.599.9
3.11-3.365.40.0768.640067480.0360.07616.7100
3.36-3.685.50.0651037036720.030.06519.8100
3.68-4.115.50.0659.534466270.030.06520.999.9
4.11-4.755.40.0649.530335580.0290.06423.4100
4.75-5.825.40.05910.325724800.0280.05920100
5.82-8.225.20.0639.220053870.030.06318.5100
8.22-26.5494.70.0579.910782300.0280.05720.797

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.28 Å25.33 Å
Translation2.28 Å25.33 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3m5n

3m5n


Resolution: 1.839→25.328 Å / FOM work R set: 0.8356 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1537 10.02 %Random
Rwork0.1927 13802 --
obs0.1979 15339 90.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.4 Å2 / Biso mean: 16.26 Å2 / Biso min: 4.08 Å2
Refinement stepCycle: final / Resolution: 1.839→25.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 98 33 1502
Biso mean--11.85 18.42 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151444
X-RAY DIFFRACTIONf_angle_d1.6211984
X-RAY DIFFRACTIONf_chiral_restr0.398240
X-RAY DIFFRACTIONf_plane_restr0.008251
X-RAY DIFFRACTIONf_dihedral_angle_d13.744552
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.839-1.89870.2973850.250975283755
1.8987-1.96650.28441070.2139971107872
1.9665-2.04520.26051310.20021167129885
2.0452-2.13820.26961380.19221245138392
2.1382-2.25090.23311420.19211294143695
2.2509-2.39180.22921490.18921338148797
2.3918-2.57630.23911530.19971365151898
2.5763-2.83530.29111530.20791370152399
2.8353-3.24480.25921550.20381391154699
3.2448-4.08540.23691560.175914061562100
4.0854-25.330.20211680.176915031671100

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