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- PDB-3gol: HCV NS5b polymerase in complex with 1,5 benzodiazepine inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 3gol
TitleHCV NS5b polymerase in complex with 1,5 benzodiazepine inhibitor (R)-11d
ComponentsRNA-directed RNA polymeraseRNA-dependent RNA polymerase
KeywordsTRANSFERASE / 1 / 5-Benzodiazepine / HCV Polymerase / NS5B / medicinal chemistry / 1b-J4
Function / homology
Function and homology information


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 / SH3 domain binding / : ...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 / SH3 domain binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / molecular adaptor activity / 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 / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
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 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-XND / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus isolate
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsNyanguile, O. / De Bondt, H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: 1,5-Benzodiazepine inhibitors of HCV NS5B polymerase.
Authors: McGowan, D. / Nyanguile, O. / Cummings, M.D. / Vendeville, S. / Vandyck, K. / Van den Broeck, W. / Boutton, C.W. / De Bondt, H. / Quirynen, L. / Amssoms, K. / Bonfanti, J.F. / Last, S. / ...Authors: McGowan, D. / Nyanguile, O. / Cummings, M.D. / Vendeville, S. / Vandyck, K. / Van den Broeck, W. / Boutton, C.W. / De Bondt, H. / Quirynen, L. / Amssoms, K. / Bonfanti, J.F. / Last, S. / Rombauts, K. / Tahri, A. / Hu, L. / Delouvroy, F. / Vermeiren, K. / Vandercruyssen, G. / Van der Helm, L. / Cleiren, E. / Mostmans, W. / Lory, P. / Pille, G. / Van Emelen, K. / Fanning, G. / Pauwels, F. / Lin, T.I. / Simmen, K. / Raboisson, P.
History
DepositionMar 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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: RNA-directed RNA polymerase
B: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,5746
Polymers129,6352
Non-polymers9394
Water2,018112
1
A: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2873
Polymers64,8171
Non-polymers4702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2873
Polymers64,8171
Non-polymers4702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.048, 106.620, 134.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-directed RNA polymerase / RNA-dependent RNA polymerase / HCV NS5B RNA POLYMERASE / NS5B / p68


Mass: 64817.262 Da / Num. of mol.: 2 / Fragment: UNP residues 2420-2989
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus isolate / Strain: HC-J4 / Gene: NS5B / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O92972, RNA-directed RNA polymerase
#2: Chemical ChemComp-XND / (11R)-10-acetyl-11-(2,4-dichlorophenyl)-6-hydroxy-3,3-dimethyl-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]diazepin-1-one


Mass: 445.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22Cl2N2O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 5-8% PEG 6000, 100mM Mg-Salts, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.85→41.81 Å / Num. all: 36205 / Num. obs: 36205 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 10.5
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3510 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→41.81 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.873 / SU B: 27.449 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 1811 5 %RANDOM
Rwork0.1883 ---
all0.19133 34394 --
obs0.19133 34394 99.64 %-
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: 33.615 Å2
Baniso -1Baniso -2Baniso -3
1-3.61 Å20 Å20 Å2
2---0.56 Å20 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.85→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8695 0 62 112 8869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228950
X-RAY DIFFRACTIONr_bond_other_d0.0010.028178
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.97412158
X-RAY DIFFRACTIONr_angle_other_deg0.785318990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60851111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59122.527364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.038151515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8031578
X-RAY DIFFRACTIONr_chiral_restr0.0710.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029865
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021841
X-RAY DIFFRACTIONr_nbd_refined0.220.22072
X-RAY DIFFRACTIONr_nbd_other0.1820.28439
X-RAY DIFFRACTIONr_nbtor_refined0.1840.24395
X-RAY DIFFRACTIONr_nbtor_other0.0880.25402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0210.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.00327153
X-RAY DIFFRACTIONr_mcbond_other0.37222235
X-RAY DIFFRACTIONr_mcangle_it2.70839006
X-RAY DIFFRACTIONr_scbond_it4.11143961
X-RAY DIFFRACTIONr_scangle_it6.1663152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 131 -
Rwork0.233 2491 -
obs--99.51 %

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