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- PDB-3oyp: HCV NS3/4A in complex with ligand 3 -

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Basic information

Entry
Database: PDB / ID: 3oyp
TitleHCV NS3/4A in complex with ligand 3
Components
  • Non-structural protein 4A
  • Peptidomimetic inhibitor
  • Serine protease NS3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / NS3 / NS4A / HEPATITIS C VIRUS / PROTEASE INHIBITION / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / RNA strand annealing activity / hepacivirin / 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 ...RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / RNA strand annealing activity / hepacivirin / 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 / 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 / protein-DNA complex / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / 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 / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / zinc ion binding / ATP binding / membrane
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 / helicase superfamily c-terminal 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 / Trypsin-like serine proteases / Helicase superfamily 1/2, ATP-binding domain / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
N-propanoyl-D-alanyl-(4R)-4-[(7-bromoisoquinolin-1-yl)oxy]-N-{(1R,2R)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-L-prolinamide / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.76 Å
AuthorsHagel, M. / Niu, D. / St.Martin, T. / Sheets, M.P. / Qiao, L. / Bernard, H. / Karp, R.M. / Zhu, Z. / Labenski, M.T. / Chaturvedi, P.C. ...Hagel, M. / Niu, D. / St.Martin, T. / Sheets, M.P. / Qiao, L. / Bernard, H. / Karp, R.M. / Zhu, Z. / Labenski, M.T. / Chaturvedi, P.C. / Nacht, M. / Westlin, W.F. / Petter, R.C. / Singh, J.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Selective irreversible inhibition of a protease by targeting a noncatalytic cysteine.
Authors: Hagel, M. / Niu, D. / St.Martin, T. / Sheets, M.P. / Qiao, L. / Bernard, H. / Karp, R.M. / Zhu, Z. / Labenski, M.T. / Chaturvedi, P. / Nacht, M. / Westlin, W.F. / Petter, R.C. / Singh, J.
History
DepositionSep 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Dec 19, 2012Group: Non-polymer description / Structure summary
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.6Sep 6, 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 / struct_conn / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease NS3
B: Serine protease NS3
C: Non-structural protein 4A
D: Non-structural protein 4A
E: Peptidomimetic inhibitor
F: Peptidomimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3558
Polymers44,2246
Non-polymers1312
Water18010
1
A: Serine protease NS3
C: Non-structural protein 4A
E: Peptidomimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1123
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-48 kcal/mol
Surface area8270 Å2
MethodPISA
2
B: Serine protease NS3
D: Non-structural protein 4A
F: Peptidomimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1123
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-47 kcal/mol
Surface area8190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.401, 94.401, 83.129
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Serine protease NS3 / Hepacivirin / NS3P / p70


Mass: 19749.553 Da / Num. of mol.: 2
Fragment: PROTEASE/HELICASE NS3 (P70), UNP residues 1027-1213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus (isolate Japanese) / Production host: Escherichia coli (E. coli)
References: UniProt: P26662, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Protein/peptide Non-structural protein 4A / NS4A / p8


Mass: 1686.097 Da / Num. of mol.: 2
Fragment: NONSTRUCTURAL PROTEIN NS4A (P4), UNP residues 1677-1991
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus (isolate Japanese) / Production host: Escherichia coli (E. coli) / References: UniProt: P26662
#3: Protein/peptide Peptidomimetic inhibitor


Type: Peptide-like / Class: AntiviralAntiviral drug / Mass: 676.579 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: N-propanoyl-D-alanyl-(4R)-4-[(7-bromoisoquinolin-1-yl)oxy]-N-{(1R,2R)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-L-prolinamide
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.51 Å3/Da / Density % sol: 51.11 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: NaCl, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: PILATUS 6M / Detector: CCD / Date: Dec 4, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.76→81.65 Å / Num. all: 10926 / Num. obs: 10926 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.123
Reflection shellResolution: 2.76→2.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.643 / % possible all: 92.6

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: 1DXP

1dxp


Resolution: 2.76→81.65 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.849 / SU B: 16.216 / SU ML: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 762 7 %RANDOM
Rwork0.21483 ---
all0.22271 10158 --
obs0.21892 10158 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.76→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 2 10 2827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222878
X-RAY DIFFRACTIONr_bond_other_d0.0050.022687
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.0113934
X-RAY DIFFRACTIONr_angle_other_deg3.42736224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.59221.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94315436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5511524
X-RAY DIFFRACTIONr_chiral_restr0.0560.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_nbd_refined0.1810.2574
X-RAY DIFFRACTIONr_nbd_other0.1760.22707
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21417
X-RAY DIFFRACTIONr_nbtor_other0.0820.21647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.320.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1450.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.19522362
X-RAY DIFFRACTIONr_mcbond_other0.1562772
X-RAY DIFFRACTIONr_mcangle_it1.51432984
X-RAY DIFFRACTIONr_scbond_it2.19441213
X-RAY DIFFRACTIONr_scangle_it3.0356938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.76→2.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 67 -
Rwork0.311 738 -
obs--99.88 %

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