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- PDB-6dir: Crystal structure of HCV NS3/4A protease in complex with P4-P5-2 ... -

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Basic information

Entry
Database: PDB / ID: 6dir
TitleCrystal structure of HCV NS3/4A protease in complex with P4-P5-2 (AJ-67)
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


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 / 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
Chem-GKA / NS3 protease
Similarity search - Component
Biological speciesHepacivirus C
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.751 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

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Assembly

Deposited unit
A: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2435
Polymers21,1751
Non-polymers1,0684
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-17 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.147, 59.810, 58.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NS3 protease


Mass: 21175.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4WYC6
#2: Chemical ChemComp-GKA / (2R,6S,12Z,13aS,14aR,16aS)-6-[(N-acetyl-3-methyl-L-valyl)amino]-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-N-[(1-methyl cyclopropyl)sulfonyl]-5,16-dioxo-1,2,3,6,7,8,9,10,11,13a,14,15,16,16a-tetradecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diaz acyclopentadecine-14a(5H)-carboxamide / P4-P5-2 (AJ-67)


Mass: 809.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H55N7O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
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: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.751→27.573 Å / Num. obs: 19508 / % possible obs: 97 % / Redundancy: 6.1 % / Net I/σ(I): 8.8
Reflection shellResolution: 1.751→1.8431 Å

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Processing

Software
NameVersionClassification
HKL-3000703xdata scaling
PHASER1.12-2829phasing
PHENIX(1.12_2829: ???)refinement
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VOJ

5voj


Resolution: 1.751→27.573 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.14
RfactorNum. reflection% reflection
Rfree0.1925 962 4.94 %
Rwork0.1459 --
obs0.1483 19463 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.751→27.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 68 232 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091568
X-RAY DIFFRACTIONf_angle_d1.2772148
X-RAY DIFFRACTIONf_dihedral_angle_d17.645914
X-RAY DIFFRACTIONf_chiral_restr0.064246
X-RAY DIFFRACTIONf_plane_restr0.007272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7509-1.84310.21461020.15012300X-RAY DIFFRACTION85
1.8431-1.95860.17811300.1412600X-RAY DIFFRACTION97
1.9586-2.10980.23021340.1372642X-RAY DIFFRACTION98
2.1098-2.3220.19421390.13362681X-RAY DIFFRACTION99
2.322-2.65780.19011450.13922693X-RAY DIFFRACTION99
2.6578-3.34760.16161540.14752734X-RAY DIFFRACTION100
3.3476-27.57690.20361580.15692851X-RAY DIFFRACTION100

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