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- PDB-2obo: Structure of HEPATITIS C VIRAL NS3 protease domain complexed with... -

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Basic information

Entry
Database: PDB / ID: 2obo
TitleStructure of HEPATITIS C VIRAL NS3 protease domain complexed with NS4A peptide and ketoamide SCH476776
Components
  • HCV NS3 protease
  • HCV NS4A peptide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ketoamide inhibitor / Viral Protein / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


self proteolysis / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / serine-type peptidase activity ...self proteolysis / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / serine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / lipid droplet / virion component / : / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / induction by virus of host autophagy / 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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
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 / 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
TERT-BUTYL [(1S)-1-{[(1R,2S,5S)-2-({[(1S)-3-AMINO-1-(CYCLOPROPYLMETHYL)-2,3-DIOXOPROPYL]AMINO}CARBONYL)-6,6-DIMETHYL-3-AZABICYCLO[3.1.0]HEX-3-YL]CARBONYL}-2,2-DIMETHYLPROPYL]CARBAMATE / BETA-MERCAPTOETHANOL / Chem-HUD / NS3 protease / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsProngay, A.J. / Guo, Z. / Yao, N. / Fischmann, T. / Strickland, C. / Myers Jr., J. / Weber, P.C. / Malcolm, B. / Beyer, B.M. / Ingram, R. ...Prongay, A.J. / Guo, Z. / Yao, N. / Fischmann, T. / Strickland, C. / Myers Jr., J. / Weber, P.C. / Malcolm, B. / Beyer, B.M. / Ingram, R. / Pichardo, J. / Hong, Z. / Prosise, W.W. / Ramanathan, L. / Taremi, S.S. / Yarosh-Tomaine, T. / Zhang, R. / Senior, M. / Yang, R. / Arasappan, A. / Bennett, F. / Bogen, S.F. / Chen, K. / Jao, E. / Liu, Y. / Love, R.G. / Saksena, A.K. / Venkatraman, S. / Girijavallabhan, V. / Njoroge, F.G. / Madison, V.
Citation
Journal: J.Med.Chem. / Year: 2007
Title: Discovery of the HCV NS3/4A protease inhibitor (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3- [2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]- 6,6- ...Title: Discovery of the HCV NS3/4A protease inhibitor (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3- [2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]- 6,6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (Sch 503034) II. Key steps in structure-based optimization.
Authors: Prongay, A.J. / Guo, Z. / Yao, N. / Pichardo, J. / Fischmann, T. / Strickland, C. / Myers Jr., J. / Weber, P.C. / Beyer, B.M. / Ingram, R. / Hong, Z. / Prosise, W.W. / Ramanathan, L. / ...Authors: Prongay, A.J. / Guo, Z. / Yao, N. / Pichardo, J. / Fischmann, T. / Strickland, C. / Myers Jr., J. / Weber, P.C. / Beyer, B.M. / Ingram, R. / Hong, Z. / Prosise, W.W. / Ramanathan, L. / Taremi, S.S. / Yarosh-Tomaine, T. / Zhang, R. / Senior, M. / Yang, R.S. / Malcolm, B. / Arasappan, A. / Bennett, F. / Bogen, S.L. / Chen, K. / Jao, E. / Liu, Y.T. / Lovey, R.G. / Saksena, A.K. / Venkatraman, S. / Girijavallabhan, V. / Njoroge, F.G. / Madison, V.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide.
Authors: Kim, J.L. / Morgenstern, K.A. / Lin, C. / Fox, T. / Dwyer, M.D. / Landro, J.A. / Chambers, S.P. / Markland, W. / Lepre, C.A. / O'Malley, E.T. / Harbeson, S.L. / Rice, C.M. / Murcko, M.A. / ...Authors: Kim, J.L. / Morgenstern, K.A. / Lin, C. / Fox, T. / Dwyer, M.D. / Landro, J.A. / Chambers, S.P. / Markland, W. / Lepre, C.A. / O'Malley, E.T. / Harbeson, S.L. / Rice, C.M. / Murcko, M.A. / Caron, P.R. / Thomson, J.A.
#2: Journal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Hepatitis C virus NS3-4A serine protease inhibitors: SAR of P'2 moiety with improved potency.
Authors: Arasappan, A. / Njoroge, F.G. / Chan, T.Y. / Bennett, F. / Bogen, S.L. / Chen, K. / Gu, H. / Hong, L. / Jao, E. / Liu, Y.T. / Lovey, R.G. / Parekh, T. / Pike, R.E. / Pinto, P. / Santhanam, B. ...Authors: Arasappan, A. / Njoroge, F.G. / Chan, T.Y. / Bennett, F. / Bogen, S.L. / Chen, K. / Gu, H. / Hong, L. / Jao, E. / Liu, Y.T. / Lovey, R.G. / Parekh, T. / Pike, R.E. / Pinto, P. / Santhanam, B. / Venkatraman, S. / Vaccaro, H. / Wang, H. / Yang, X. / Zhu, Z. / Mckittrick, B. / Saksena, A.K. / Girijavallabhan, V. / Pichardo, J. / Butkiewicz, N. / Ingram, R. / Malcolm, B. / Prongay, A. / Yao, N. / Marten, B. / Madison, V. / Kemp, S. / Levy, O. / Lim-Wilby, M. / Tamura, S. / Ganguly, A.K.
#3: Journal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Synthesis and biological activity of macrocyclic inhibitors of hepatitis C virus (HCV) NS3 protease.
Authors: Chen, K.X. / Njoroge, F.G. / Prongay, A. / Pichardo, J. / Madison, V. / Girijavallabhan, V.
#4: Journal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Hepatitis C virus NS3-4A serine protease inhibitors: use of a P2-P1 cyclopropyl alanine combination for improved potency.
Authors: Bogen, S. / Saksena, A.K. / Arasappan, A. / Gu, H. / Njoroge, F.G. / Girijavallabhan, V. / Pichardo, J. / Butkiewicz, N. / Prongay, A. / Madison, V.
#5: Journal: J.Biol.Chem. / Year: 2006
Title: Mutations conferring resistance to SCH6, a novel hepatitis C virus NS3/4A protease inhibitor. Reduced RNA replication fitness and partial rescue by second-site mutations.
Authors: Yi, M. / Tong, X. / Skelton, A. / Chase, R. / Chen, T. / Prongay, A. / Bogen, S.L. / Saksena, A.K. / Njoroge, F.G. / Veselenak, R.L. / Pyles, R.B. / Bourne, N. / Malcolm, B.A. / Lemon, S.M.
History
DepositionDec 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Dec 26, 2012Group: Database references / Non-polymer description ...Database references / Non-polymer description / Source and taxonomy / Structure summary
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HCV NS3 protease
B: HCV NS4A peptide
C: HCV NS3 protease
D: HCV NS4A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9728
Polymers47,2554
Non-polymers7184
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-125 kcal/mol
Surface area15660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)224.271, 224.271, 75.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein HCV NS3 protease


Mass: 21233.225 Da / Num. of mol.: 2 / Fragment: UNP residues 1027 1207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Gene: HCV / Production host: Escherichia coli (E. coli) / References: UniProt: Q91RS4
#2: Protein/peptide HCV NS4A peptide


Mass: 2394.039 Da / Num. of mol.: 2 / Fragment: UNP residues 1678 1696 / Mutation: C22S / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: Q9QP06

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Non-polymers , 4 types, 139 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-HUD / tert-butyl {(2S)-1-[(1R,2S,5S)-2-{[(2S,3R)-4-amino-1-cyclopropyl-3-hydroxy-4-oxobutan-2-yl]carbamoyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hex-3-yl]-3,3-dimethyl-1-oxobutan-2-yl}carbamate / ketoamide inhibitor SCH476776, bound form


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 508.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H44N4O6
References: TERT-BUTYL [(1S)-1-{[(1R,2S,5S)-2-({[(1S)-3-AMINO-1-(CYCLOPROPYLMETHYL)-2,3-DIOXOPROPYL]AMINO}CARBONYL)-6,6-DIMETHYL-3-AZABICYCLO[3.1.0]HEX-3-YL]CARBONYL}-2,2-DIMETHYLPROPYL]CARBAMATE
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsUPON BINDING TO SER A139 THE ALDEHYDE GROUP OF THE STARTING MOLECULE HUD FORMS A HEMIACETAL BONDING ...UPON BINDING TO SER A139 THE ALDEHYDE GROUP OF THE STARTING MOLECULE HUD FORMS A HEMIACETAL BONDING WITH THE PROTEIN

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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: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: The protein (NS3 complexed with KK-NS4a(21-39)-KK peptide) was at 12-15 mg/ml in 15 mM MES, pH 6.5 1 M NaCl 20 mM b-mercaptoethanol. Hanging Drops were formed by mixing 4:l protein solution ...Details: The protein (NS3 complexed with KK-NS4a(21-39)-KK peptide) was at 12-15 mg/ml in 15 mM MES, pH 6.5 1 M NaCl 20 mM b-mercaptoethanol. Hanging Drops were formed by mixing 4:l protein solution with 4:l {0.75-1.0 M NaCl, 0.1M Na/K phosphate 0.1 M Mes, pH 5.8-6.1 20 mM b-mercaptoethanol} The drop was equilibrated the drops over 1 ml {(1.25-1.50 M) NaCl - 0.1M Na/K phosphate 0.1 M Mes, pH 5.6-5.8, 20 mM b-mercaptoethanol} , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 22055 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 2.2 % / Biso Wilson estimate: 27.999 Å2 / Rsym value: 0.069
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1443 / Rsym value: 0.466 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
X-PLORmodel building
X-PLOR98.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB Entry 2O8M

2o8m


Resolution: 2.6→8 Å
RfactorNum. reflection
Rfree0.295 1393
Rwork0.178 -
obs-14291
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 42 135 2935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.937
X-RAY DIFFRACTIONx_improper_angle_d1.497
LS refinement shellResolution: 2.6→2.71 Å
RfactorNum. reflection% reflection
Rfree0.2807 104 -
Rwork0.4102 --
obs-1025 78.2 %

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