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- PDB-6diw: Crystal structure of HCV NS3/4A D168A protease in complex with P4... -

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Basic information

Entry
Database: PDB / ID: 6diw
TitleCrystal structure of HCV NS3/4A D168A protease in complex with P4-1 (AJ-71)
ComponentsNS3 protease
KeywordsHYDROLASE/HYDROLASE Inhibitor / NS3/4a Protease / Hepatitis C virus / Drug Resistance / Protease inhibitor / HYDROLASE-HYDROLASE Inhibitor complex / HYDROLASE
Function / homology
Function and homology information


symbiont-mediated transformation of host cell / host cell membrane / serine-type peptidase activity / host cell / symbiont entry into host cell / virion attachment to host cell / virion membrane / proteolysis / metal ion binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
1,1,1-trifluoro-2-methylpropan-2-yl / NS3 protease
Similarity search - Component
Biological speciesHepacivirus C
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMatthew, A.N. / Schiffer, C.A.
Funding support United States, 2items
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
CitationJournal: To Be Published
Title: Design of Hepatitis C NS3/4A Protease Inhibitors Leveraging Untapped Regions of the Substrate Envelope
Authors: Matthew, A.N. / Schiffer, C.A.
History
DepositionMay 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,85012
Polymers21,1311
Non-polymers1,71911
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-39 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.748, 58.591, 60.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NS3 protease


Mass: 21130.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Plasmid: PET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4WYC6

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Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-GKG / 1,1,1-trifluoro-2-methylpropan-2-yl [(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 / P4-1 (AJ-71)


Mass: 808.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H47F3N6O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→26.456 Å / Num. obs: 17476 / % possible obs: 92.6 % / Redundancy: 6.9 % / Net I/σ(I): 6.3
Reflection shellResolution: 1.8→1.849 Å

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Processing

Software
NameVersionClassification
HKL-3000703xdata scaling
PHASERphasing
PHENIX1.12-2829refinement
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VOJ

5voj


Resolution: 1.8→26.456 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.61
RfactorNum. reflection% reflection
Rfree0.18 1763 10.12 %
Rwork0.138 --
obs0.1422 17417 92.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→26.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 107 257 1826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011764
X-RAY DIFFRACTIONf_angle_d1.4912427
X-RAY DIFFRACTIONf_dihedral_angle_d17.9751022
X-RAY DIFFRACTIONf_chiral_restr0.067261
X-RAY DIFFRACTIONf_plane_restr0.008303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.8490.2385820.1675818X-RAY DIFFRACTION64
1.849-1.90330.20871340.14351104X-RAY DIFFRACTION86
1.9033-1.96480.16681390.12911186X-RAY DIFFRACTION93
1.9648-2.0350.18061430.12651181X-RAY DIFFRACTION94
2.035-2.11640.17271320.13031206X-RAY DIFFRACTION94
2.1164-2.21270.19721280.12811233X-RAY DIFFRACTION95
2.2127-2.32930.17771350.12331238X-RAY DIFFRACTION95
2.3293-2.47510.15931380.12681222X-RAY DIFFRACTION96
2.4751-2.6660.19141330.13481255X-RAY DIFFRACTION96
2.666-2.9340.17721430.13941262X-RAY DIFFRACTION97
2.934-3.35790.15371460.13811285X-RAY DIFFRACTION98
3.3579-4.22780.15051560.1221300X-RAY DIFFRACTION98
4.2278-26.45840.22651540.17281364X-RAY DIFFRACTION97

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