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- PDB-6ue3: Crystal structure of HCV NS3/4A D168A protease in complex with PC... -

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Basic information

Entry
Database: PDB / ID: 6ue3
TitleCrystal structure of HCV NS3/4A D168A protease in complex with PC (JZ01-15)
ComponentsNS3 protease
KeywordsANTIVIRAL PROTEIN / Drug Resistance / Protease inhibitor / HYDROLASE-HYDROLASE Inhibitor complex / HYDROLASE / VIRAL PROTEIN
Function / homologyThrombin, subunit H - #120 / Trypsin-like serine proteases / Thrombin, subunit H / Beta Barrel / Mainly Beta / Chem-9H4
Function and homology information
Biological speciesHepacivirus C
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsZephyr, J. / Schiffer, C.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI085051 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM119345 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM131635-01 United States
CitationJournal: Mbio / Year: 2020
Title: Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors.
Authors: Matthew, A.N. / Zephyr, J. / Nageswara Rao, D. / Henes, M. / Kamran, W. / Kosovrasti, K. / Hedger, A.K. / Lockbaum, G.J. / Timm, J. / Ali, A. / Kurt Yilmaz, N. / Schiffer, C.A.
History
DepositionSep 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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)22,66311
Polymers21,2181
Non-polymers1,44510
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.616, 58.511, 59.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NS3 protease


Mass: 21218.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 213 molecules

#2: Chemical ChemComp-9H4 / tert-butyl [(2R,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6-yl]carbamate


Mass: 754.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H50N6O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20-26% PEG 3350, 0.1 M sodium MES pH 6.5, 1-4% ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.56→26.7 Å / Num. obs: 28103 / % possible obs: 98.3 % / Redundancy: 8.9 % / Biso Wilson estimate: 11.32 Å2 / Rsym value: 0.047 / Net I/σ(I): 25.2
Reflection shellResolution: 1.56→1.59 Å / Num. unique obs: 1114 / Rsym value: 0.143

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000V703Xdata scaling
PHASERphasing
Coot0.8.8model building
HKL-3000V703Xdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VOJ

5voj


Resolution: 1.56→26.29 Å / SU ML: 0.1044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.831
RfactorNum. reflection% reflection
Rfree0.181 1421 5.07 %
Rwork0.1554 --
obs0.1567 28029 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.64 Å2
Refinement stepCycle: LAST / Resolution: 1.56→26.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 0 92 203 1707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01031572
X-RAY DIFFRACTIONf_angle_d1.50212144
X-RAY DIFFRACTIONf_chiral_restr0.0632247
X-RAY DIFFRACTIONf_plane_restr0.0079268
X-RAY DIFFRACTIONf_dihedral_angle_d9.29661202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.620.18751250.17152269X-RAY DIFFRACTION85.07
1.62-1.680.20971340.16452646X-RAY DIFFRACTION98.72
1.68-1.760.19991350.15532660X-RAY DIFFRACTION99.64
1.76-1.850.18761440.15272659X-RAY DIFFRACTION100
1.85-1.970.18911370.14442688X-RAY DIFFRACTION100
1.97-2.120.16431410.14122682X-RAY DIFFRACTION100
2.12-2.330.1711490.13972714X-RAY DIFFRACTION100
2.33-2.670.19161420.15082701X-RAY DIFFRACTION100
2.67-3.360.16361550.1592739X-RAY DIFFRACTION99.93
3.36-26.290.18451590.16832850X-RAY DIFFRACTION99.41

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