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- PDB-6pj0: Crystal structure of HCV NS3/4A D168A protease in complex with P4... -

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Basic information

Entry
Database: PDB / ID: 6pj0
TitleCrystal structure of HCV NS3/4A D168A protease in complex with P4-5 (NR01-97)
ComponentsNS3/4 Aprotease
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
Chem-OMV / NS3 protease
Similarity search - Component
Biological speciesHepacivirus C
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
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: NS3/4 Aprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4917
Polymers23,3481
Non-polymers1,1436
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.169, 58.515, 59.646
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 NS3/4 Aprotease


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, 108 molecules

#2: Chemical ChemComp-OMV / 1-ethylcyclopentyl [(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 / P4-5 (NR01-97)


Mass: 794.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54N6O9S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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.: 102 / 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: 2.13 Å3/Da / Density % sol: 42.4 %
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: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 12209 / % possible obs: 99.1 % / Redundancy: 6 % / Net I/σ(I): 18.7
Reflection shellResolution: 2.07→2.11 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: 2.05→26.27 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.08
RfactorNum. reflection% reflection
Rfree0.221 612 5.01 %
Rwork0.182 --
obs0.184 12206 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→26.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 74 102 1577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031524
X-RAY DIFFRACTIONf_angle_d0.8222086
X-RAY DIFFRACTIONf_dihedral_angle_d6.6481168
X-RAY DIFFRACTIONf_chiral_restr0.048244
X-RAY DIFFRACTIONf_plane_restr0.004264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0544-2.2610.22941490.18222778X-RAY DIFFRACTION97
2.261-2.5880.26531510.18962868X-RAY DIFFRACTION100
2.588-3.25960.24291550.19142905X-RAY DIFFRACTION100
3.2596-26.26970.19191570.17363043X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.038 Å / Origin y: -22.1395 Å / Origin z: 8.5107 Å
111213212223313233
T0.1489 Å20.0016 Å20.0063 Å2-0.1284 Å20.0058 Å2--0.1379 Å2
L2.1741 °2-0.0778 °20.7929 °2-1.3446 °2-0.0101 °2--1.476 °2
S0.0173 Å °-0.0369 Å °-0.0163 Å °-0.0299 Å °0.0022 Å °-0.0585 Å °0.0066 Å °-0.0097 Å °-0.0191 Å °
Refinement TLS groupSelection details: ALL

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