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- PDB-6pj2: Crystal structure of HCV NS3/4A D168A protease in complex with P4... -

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Basic information

Entry
Database: PDB / ID: 6pj2
TitleCrystal structure of HCV NS3/4A D168A protease in complex with P4-P5-4 (AJ-65)
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-OM7 / NS3 protease
Similarity search - Component
Biological speciesHepacivirus C
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJun 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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)24,5688
Polymers23,3481
Non-polymers1,2207
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.364, 59.637, 58.587
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: 23348.418 Da / Num. of mol.: 1 / Mutation: D168A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Plasmid: PET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B4WYC6

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Non-polymers , 5 types, 114 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OM7 / (2R,6S,12Z,13aS,14aR,16aS)-6-[(N-acetyl-L-isoleucyl)amino]-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-N-[(1-methylcyclo propyl)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]diazacycl opentadecine-14a(5H)-carboxamide / P4-P5-4 (AJ-65)


Mass: 809.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H55N7O9S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
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 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 11513 / % possible obs: 99.1 % / Redundancy: 6.7 % / Net I/σ(I): 16.6
Reflection shellResolution: 2.1→2.14 Å

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Processing

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

5voj


Resolution: 2.1→26.29 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.37
RfactorNum. reflection% reflection
Rfree0.214 575 4.99 %
Rwork0.182 --
obs0.184 11513 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→26.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 79 107 1587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021518
X-RAY DIFFRACTIONf_angle_d0.7612075
X-RAY DIFFRACTIONf_dihedral_angle_d6.6461160
X-RAY DIFFRACTIONf_chiral_restr0.05245
X-RAY DIFFRACTIONf_plane_restr0.003263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0994-2.31060.21441350.192641X-RAY DIFFRACTION97
2.3106-2.64470.23251430.19452682X-RAY DIFFRACTION99
2.6447-3.33090.22141420.18872754X-RAY DIFFRACTION100
3.3309-26.29490.20331550.17172861X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.8329 Å / Origin y: 6.3921 Å / Origin z: -7.6421 Å
111213212223313233
T0.1548 Å20.0022 Å2-0.006 Å2-0.1467 Å2-0.0039 Å2--0.1319 Å2
L1.487 °2-0.6174 °2-0.1359 °2-1.3312 °20.0017 °2--0.9811 °2
S0.0037 Å °0.0416 Å °-0.0212 Å °-0.0156 Å °-0.0054 Å °0.0033 Å °-0.0199 Å °0.0571 Å °-0.0057 Å °
Refinement TLS groupSelection details: ALL

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