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- PDB-2f9v: HCV NS3 protease domain with NS4a peptide and a ketoamide inhibit... -

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Basic information

Entry
Database: PDB / ID: 2f9v
TitleHCV NS3 protease domain with NS4a peptide and a ketoamide inhibitor with P1 and P2 cyclopropylalannines
Components
  • NS3 protease/helicase
  • polyprotein
KeywordsVIRAL PROTEIN / HCV / Hepatitis C protease / NS3 protease / ketoamide inhibitor
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 / fatty acid biosynthetic process / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-BN6 / : / : / Lipoxygenase
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsBogen, S.L. / Ruan, S. / Liu, R. / Agrawal, S. / Pichardo, J. / Prongay, A. / Baroudy, B. / Saksena, A. / Girijavallabhan, V. / Njoroge, F.G.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Depeptidization efforts on P3-P2 a-ketoamide inhibitors of HCV NS3-4A serine protease: Effect on HCV replicon activity.
Authors: Bogen, S.L. / Ruan, S. / Liu, R. / Agrawal, S. / Pichardo, J. / Prongay, A. / Baroudy, B. / Saksena, A. / Girijavallabhan, V. / Njoroge, F.G.
#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: Use of a P2-P1 cyclopropyl alanine combination to improve potency.
Authors: Bogen, S. / Saksena, A.K. / Arasappan, A. / Gu, N. / Njoroge, F.G. / Girijavallabhan, V. / Pichardo, J. / Butkiewicz, N. / Prongay, A. / Madison, A.
#3: Journal: J.Med.Chem. / Year: 2005
Title: Design and Synthesis of Depeptidized Macrocyclic Inhibitors of Hepatitis C NS3-4A Protease Using Structure-Based Drug Design
Authors: Venkatraman, S. / Njoroge, F.G. / Girijavallabhan, V.M. / Madison, V.S. / Yao, N.H. / Prongay, A.J. / Butkiewicz, N. / Pichardo, J.
#4: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2005
Title: Proline-Based Macrocyclic Inhibitors of the Hepatitis C Virus: Stereoselective Synthesis and Biological Activity.
Authors: Chen, K.X. / Njoroge, F.G. / Vibulbhan, B. / Prongay, A. / Pichardo, J. / Madison, V. / Buevich, A. / Chan, T.M.
#5: Journal: Bioorg.Med.Chem.Lett. / Year: 2004
Title: Novel 2-oxoimidazolidine-4-carboxylic acid derivatives as Hepatitis C virus NS3-4A serine protease inhibitors: synthesis, activity and X-ray crystal structure of an enzyme inhibitor complex
Authors: Arasappan, A. / Njoroge, F.G. / Parekh, T.N. / Yang, X. / Pichardo, J. / Butkiewicz, N. / Prongay, A. / Yao, N. / Girijavallabhan, V.
History
DepositionDec 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.ptnr2_label_seq_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
Revision 1.4Mar 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / pdbx_entity_src_syn
Item: _entity.details
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS3 protease/helicase
B: polyprotein
C: NS3 protease/helicase
D: polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2007
Polymers47,3694
Non-polymers8323
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-129 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.811, 222.811, 75.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe NS3 protease domain, residues 1-181 of NS3, exists in a complex with an NS4a peptide and an inhibitor. There is a dimer of the NS3 domain-NS4a peptide complex, but only one monomer (Chains A and B) have the inhibitor bound to the active site. This dimer is the component of the asymmetric unit. In vivo, the protease domain is part of a multi enzyme protein (having both protease and helicase activities). The NS3 protease domain with the NS4A peptide is known to be catalytically active in the absence of the helicase domain, although it is not known whether it is active as a monomer or dimer.

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Components

#1: Protein NS3 protease/helicase


Mass: 21290.277 Da / Num. of mol.: 2 / Fragment: protease domain (Residues : 1-181)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Strain: H
Gene: NS3 protease domain ( residues 1027-1207 of the polyprotein).
Plasmid: NS3(181)His6/pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: GenBank: 28921568, UniProt: P27958*PLUS
#2: Protein/peptide polyprotein


Mass: 2394.039 Da / Num. of mol.: 2 / Fragment: Residues 21-39 / Source method: obtained synthetically
Details: Solid-phase peptide synthesis of the NS4a residues 21-39 peptide with N-terminal KK and C-terminal KK extensions.
References: GenBank: 51039195, UniProt: P27958*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Details: ketoamide peptide
#4: Chemical ChemComp-BN6 / (2S,8R,9S,15S)-15-CYCLOHEXYL-9,12-BIS(CYCLOPROPYLMETHYL)-8-HYDROXY-20-METHYL-4,7,11,14,17-PENTAOXO-2-PHENYL-18-OXA-3,6,10,12,13,16-HEXAAZAHENICOSAN-1-OIC ACID


Mass: 700.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H52N6O9
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 285 K / pH: 5.7
Details: 12-15 mG/mL Protein in 15 mM MES, pH 6.5 - 1.0 M NaCl equivolume mixture with (0.85-1.05M) NaCl- 0.1M MES-0.1 M Na/KPO4, pH5.5-5.8 - 5mM BME, equilibrated with 1.35-1.55M NaCl-0.1M MES-0.1M ...Details: 12-15 mG/mL Protein in 15 mM MES, pH 6.5 - 1.0 M NaCl equivolume mixture with (0.85-1.05M) NaCl- 0.1M MES-0.1 M Na/KPO4, pH5.5-5.8 - 5mM BME, equilibrated with 1.35-1.55M NaCl-0.1M MES-0.1M Na/KPO4, pH 5.6-5.8 - 5 mM BME, VAPOR DIFFUSION, HANGING DROP, temperature 285K, pH 5.70

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 27, 2000 / Details: OSMIC GREEN
RadiationMonochromator: OSMIC GREEN / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→2.69 Å / Num. obs: 21990 / % possible obs: 99.7 % / Observed criterion σ(I): 1.97 / Redundancy: 3.7 % / Biso Wilson estimate: 37.31 Å2 / Rsym value: 0.088 / Net I/σ(I): 16.8
Reflection shellResolution: 2.6→2.69 Å / Rsym value: 0.551 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR98.1refinement
HKL-2000data reduction
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→2.69 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1983 9.4 %RANDOM
Rwork0.189 ---
obs0.189 19887 93.8 %-
all-21990 --
Refinement stepCycle: LAST / Resolution: 2.6→2.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 52 132 2928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3453 184 7.8 %
Rwork0.3094 1906 -
obs--80.2 %

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