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

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Basic information

Entry
Database: PDB / ID: 6bqj
TitleCRYSTAL STRUCTURE OF HEPATIS C VIRUS PROTEASE (NS3) COMPLEXED WITH TRIPEPTIDIC ACYL SULFONAMIDE INHIBITOR (COMPOUND 16)
ComponentsNS3 protease
KeywordsHYDROLASE / SERINE PROTEASE / VIRAL PROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / oxylipin biosynthetic process / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / transformation of host cell by virus / host cell membrane / serine-type peptidase activity / virion component / fatty acid biosynthetic process / symbiont entry into host cell ...Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / oxylipin biosynthetic process / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / transformation of host cell by virus / host cell membrane / serine-type peptidase activity / virion component / fatty acid biosynthetic process / symbiont entry into host cell / virion attachment to host cell / proteolysis / membrane / metal ion binding / cytoplasm
Similarity search - Function
Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily ...Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / 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
ACETATE ION / Chem-Z1B / NS3 / Lipoxygenase
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.69 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 1.1Sep 4, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.2Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS3 protease
B: NS3 protease
C: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,84618
Polymers69,7843
Non-polymers3,06315
Water5,603311
1
A: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2826
Polymers23,2611
Non-polymers1,0215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2235
Polymers23,2611
Non-polymers9624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3417
Polymers23,2611
Non-polymers1,0806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.440, 57.470, 89.830
Angle α, β, γ (deg.)90.00, 115.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein NS3 protease


Mass: 23261.316 Da / Num. of mol.: 3
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

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Non-polymers , 5 types, 326 molecules

#2: Chemical ChemComp-Z1B / N-(tert-butoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(2S)-1-[(cyclopropylsulfonyl)amino]-4,4-difluoro-1-oxobutan-2-yl}-4-[(7-methoxy-2-phenylquinolin-4-yl)oxy]-L-prolinamide


Mass: 801.896 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H49F2N5O9S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 91563 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 25.21 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.6
Reflection shellResolution: 3.88→50 Å / Redundancy: 4 % / Rmerge(I) obs: 0.047 / Mean I/σ(I) obs: 23.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER2.11.7refinement
RefinementResolution: 1.69→24.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.079 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4582 5 %RANDOM
Rwork0.197 ---
obs0.197 91563 99.7 %-
Displacement parametersBiso mean: 27.09 Å2
Baniso -1Baniso -2Baniso -3
1--1.1399 Å20 Å2-0.8919 Å2
2--2.981 Å20 Å2
3----1.8412 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.69→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 180 311 4747
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014540HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.066222HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1497SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes837HARMONIC5
X-RAY DIFFRACTIONt_it4540HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.95
X-RAY DIFFRACTIONt_other_torsion13.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion634SEMIHARMONIC5
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_contact5499SEMIHARMONIC4
LS refinement shellResolution: 1.69→1.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2654 299 4.53 %
Rwork0.2405 6304 -
all0.2416 6603 -
obs--97.56 %

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