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- PDB-6mvk: HCV NS5B 1b N316 bound to Compound 18 -

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Basic information

Entry
Database: PDB / ID: 6mvk
TitleHCV NS5B 1b N316 bound to Compound 18
ComponentsHCV Polymerase
KeywordsVIRAL PROTEIN / Hepatitus C / NS5B
Function / homology
Function and homology information


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 / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity ...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 / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / ribonucleoprotein complex / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / 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 NS2, C-terminal domain / 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, 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 NS2, C-terminal domain / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / 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 zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepatitis C virus, Non-structural protein NS2 / : / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus non-structural 5a protein membrane anchor / 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 / Hepacivirus/Pegivirus NS3 protease domain profile. / Hepatitis C virus NS3 protease / Reverse transcriptase/Diguanylate cyclase domain / 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 / Alpha-Beta Plaits / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-K4J / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus subtype 1b
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Model detailsHCV NS5B 1b N316 bound to Compound 18
AuthorsWilliams, S.P. / Kahler, K. / Price, D.J. / Peat, A.J.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Design of N-Benzoxaborole Benzofuran GSK8175-Optimization of Human Pharmacokinetics Inspired by Metabolites of a Failed Clinical HCV Inhibitor.
Authors: Chong, P.Y. / Shotwell, J.B. / Miller, J. / Price, D.J. / Maynard, A. / Voitenleitner, C. / Mathis, A. / Williams, S. / Pouliot, J.J. / Creech, K. / Wang, F. / Fang, J. / Zhang, H. / Tai, V. ...Authors: Chong, P.Y. / Shotwell, J.B. / Miller, J. / Price, D.J. / Maynard, A. / Voitenleitner, C. / Mathis, A. / Williams, S. / Pouliot, J.J. / Creech, K. / Wang, F. / Fang, J. / Zhang, H. / Tai, V.W. / Turner, E. / Kahler, K.M. / Crosby, R. / Peat, A.J.
History
DepositionOct 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HCV Polymerase
B: HCV Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0164
Polymers124,9512
Non-polymers1,0652
Water6,251347
1
A: HCV Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0082
Polymers62,4761
Non-polymers5321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HCV Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0082
Polymers62,4761
Non-polymers5321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.372, 107.468, 126.744
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HCV Polymerase


Mass: 62475.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus subtype 1b / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99AU2
#2: Chemical ChemComp-K4J / (4-{(4S)-3-[5-cyclopropyl-2-(4-fluorophenyl)-3-(methylcarbamoyl)-1-benzofuran-6-yl]-2-oxo-1,3-oxazolidin-4-yl}-2-fluorophenyl)boronic acid


Mass: 532.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H23BF2N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.35 Å3/Da / Density % sol: 47.75 % / Mosaicity: 0.961 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Na Citrate pH5.0, 10% glycerol, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 52919 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.105 / Χ2: 0.893 / Net I/σ(I): 5.4 / Num. measured all: 378618
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.3-2.346.90.4726370.673199.8
2.34-2.3870.40425810.706199.8
2.38-2.437.10.3726160.676199.8
2.43-2.487.10.33826210.6861100
2.48-2.537.10.27326140.691199.9
2.53-2.597.10.26526040.6951100
2.59-2.657.20.23526260.705199.9
2.65-2.737.30.20126160.787199.8
2.73-2.817.30.1726580.7381100
2.81-2.97.30.14326230.7581100
2.9-37.40.1326270.7581100
3-3.127.40.11126450.7981100
3.12-3.267.40.09626400.8411100
3.26-3.437.30.08426500.935199.9
3.43-3.656.50.07725191.061195
3.65-3.937.20.0826721.4161100
3.93-4.337.20.07726801.551100
4.33-4.957.30.06726871.3541100
4.95-6.237.20.05927370.9811100
6.23-306.80.04428661.0091100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.6.0081refinement
PDB_EXTRACT3.24data extraction
REFMAC5.6.0081phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.75 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.503 / SU ML: 0.135 / SU R Cruickshank DPI: 0.0833 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.05
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3903 7.4 %RANDOM
Rwork0.2075 ---
obs0.2097 48865 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.43 Å2 / Biso mean: 24.545 Å2 / Biso min: 10.31 Å2
Baniso -1Baniso -2Baniso -3
1--11.3 Å20 Å20 Å2
2--25.46 Å20 Å2
3----14.16 Å2
Refinement stepCycle: final / Resolution: 2.3→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8388 0 78 347 8813
Biso mean--39.59 26.31 -
Num. residues----1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228662
X-RAY DIFFRACTIONr_bond_other_d0.0020.025740
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.9711805
X-RAY DIFFRACTIONr_angle_other_deg1.133313988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.07451094
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25123.095336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.867151374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9951557
X-RAY DIFFRACTIONr_chiral_restr0.0520.21347
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219631
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021750
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 0 Å2 / Rms dev position: 0 Å / Weight Biso : 0 / Weight position: 0
LS refinement shellResolution: 2.299→2.358 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 260 -
Rwork0.255 3361 -
all-3621 -
obs--94.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2855-0.07830.23510.1094-0.090.70050.0646-0.02590.0148-0.0038-0.029-0.00820.0832-0.0241-0.03560.0256-0.0249-0.00450.04580.00820.008311.48846.27647.39
20.35990.0640.18130.13910.08190.66890.050.024-0.00680.0049-0.01180.01950.04750.0249-0.03820.01230.0178-0.00350.0451-0.00490.0068-11.5246.39-7.692
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 563
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION2B1 - 562
4X-RAY DIFFRACTION2B601

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