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- PDB-6bqk: CRYSTAL STRUCTURE OF HEPATIS C VIRUS PROTEASE (NS3) COMPLEXED WIT... -

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Basic information

Entry
Database: PDB / ID: 6bqk
TitleCRYSTAL STRUCTURE OF HEPATIS C VIRUS PROTEASE (NS3) COMPLEXED WITH TRIPEPTIDIC ACYL SULFONAMIDE INHIBITOR (COMPOUND 18)
ComponentsNS3 protease
KeywordsHYDROLASE / SERINE PROTEASE / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / host cell membrane / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endoplasmic reticulum-Golgi intermediate compartment membrane / serine-type peptidase activity / virion component / SH3 domain binding / kinase binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont entry into host cell / ribonucleoprotein complex / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal ...Thrombin, subunit H - #120 / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-Z1E / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKlei, H.E. / Sack, J.S.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Potent Inhibitors of Hepatitis C Virus NS3 Protease: Employment of a Difluoromethyl Group as a Hydrogen-Bond Donor.
Authors: Zheng, B. / D'Andrea, S.V. / Sun, L.Q. / Wang, A.X. / Chen, Y. / Hrnciar, P. / Friborg, J. / Falk, P. / Hernandez, D. / Yu, F. / Sheaffer, A.K. / Knipe, J.O. / Mosure, K. / Rajamani, R. / ...Authors: Zheng, B. / D'Andrea, S.V. / Sun, L.Q. / Wang, A.X. / Chen, Y. / Hrnciar, P. / Friborg, J. / Falk, P. / Hernandez, D. / Yu, F. / Sheaffer, A.K. / Knipe, J.O. / Mosure, K. / Rajamani, R. / Good, A.C. / Kish, K. / Tredup, J. / Klei, H.E. / Paruchuri, M. / Ng, A. / Gao, Q. / Rampulla, R.A. / Mathur, A. / Meanwell, N.A. / McPhee, F. / Scola, P.M.
History
DepositionNov 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1986
Polymers46,5232
Non-polymers1,6754
Water2,684149
1
A: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0993
Polymers23,2611
Non-polymers8382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0993
Polymers23,2611
Non-polymers8382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.650, 68.060, 61.460
Angle α, β, γ (deg.)90.00, 109.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NS3 protease


Mass: 23261.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A075D220, UniProt: P27958*PLUS
#2: Chemical ChemComp-Z1E / N-(tert-butoxycarbonyl)-3-methyl-L-valyl-(4R)-4-[(7-chloro-4-methoxyisoquinolin-1-yl)oxy]-N-[(1R,2R)-1-[(cyclopropylsulfonyl)carbamoyl]-2-(difluoromethyl)cyclopropyl]-L-prolinamide


Mass: 772.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H44ClF2N5O9S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 26030 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15.86 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 9
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3 / % possible all: 96.6

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→23.2 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.851 / SU R Cruickshank DPI: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.236 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1255 4.83 %RANDOM
Rwork0.254 ---
obs0.254 25964 96.2 %-
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.9406 Å20 Å2-2.9192 Å2
2--3.4883 Å20 Å2
3---3.4522 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 1.97→23.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 106 149 3033
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012941HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124037HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d985SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes526HARMONIC5
X-RAY DIFFRACTIONt_it2941HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion16.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion408SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3364SEMIHARMONIC4
LS refinement shellResolution: 1.97→2.05 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2646 150 5.24 %
Rwork0.2392 2710 -
all0.2405 2860 -
obs--93.73 %

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