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- PDB-4tn2: NS5b in complex with lactam-thiophene carboxylic acids -

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Basic information

Entry
Database: PDB / ID: 4tn2
TitleNS5b in complex with lactam-thiophene carboxylic acids
ComponentsGenome polyprotein
KeywordsHYDROLASE / complex polymerase inhbitor
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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / 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. / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-33J / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis B virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChopra, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Design and synthesis of lactam-thiophene carboxylic acids as potent hepatitis C virus polymerase inhibitors.
Authors: Barnes-Seeman, D. / Boiselle, C. / Capacci-Daniel, C. / Chopra, R. / Hoffmaster, K. / Jones, C.T. / Kato, M. / Lin, K. / Ma, S. / Pan, G. / Shu, L. / Wang, J. / Whiteman, L. / Xu, M. / Zheng, R. / Fu, J.
History
DepositionJun 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Jun 1, 2016Group: Data collection
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5592
Polymers64,1901
Non-polymers3691
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.191, 159.191, 71.226
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Detailsbiological unit is the same as asym.

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Components

#1: Protein Genome polyprotein


Mass: 64189.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hepatitis B virus / References: UniProt: P26663*PLUS
#2: Chemical ChemComp-33J / 3-[(2R)-2-cyclohexyl-5-oxopyrrolidin-1-yl]-5-phenylthiophene-2-carboxylic acid


Mass: 369.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23NO3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 4.06 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 85mM Hepes, pH7.5, 1.7% PEG400, 1.7 MAS, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.67→79.6 Å / Num. obs: 29058 / % possible obs: 99.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 68.41 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.054 / Net I/σ(I): 26.2 / Num. measured all: 380742 / Scaling rejects: 1866
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.67-2.897.20.4295.34080057050.8890.16795.5
7.07-79.614.70.04574.72448916670.9950.01299.9

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Processing

Software
NameVersionClassification
XDS0.1.27data reduction
BUSTER-TNTBUSTER 2.11.4refinement
PDB_EXTRACT3.14data extraction
BUSTER2.11.4refinement
XSCALEdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.9 Å / Cor.coef. Fo:Fc: 0.9194 / Cor.coef. Fo:Fc free: 0.8961 / SU R Cruickshank DPI: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.388 / SU Rfree Blow DPI: 0.262 / SU Rfree Cruickshank DPI: 0.267
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 1411 5.02 %RANDOM
Rwork0.2204 ---
obs0.2218 28086 98.83 %-
Displacement parametersBiso max: 144.98 Å2 / Biso mean: 42.73 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.2041 Å20 Å20 Å2
2--0.2041 Å20 Å2
3----0.4082 Å2
Refine analyzeLuzzati coordinate error obs: 0.387 Å
Refinement stepCycle: final / Resolution: 2.7→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 26 127 4514
Biso mean--39.03 41.3 -
Num. residues----561
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1552SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes660HARMONIC5
X-RAY DIFFRACTIONt_it4485HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion588SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5144SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4485HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6086HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion17.46
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3057 149 5.55 %
Rwork0.2574 2535 -
all0.2599 2684 -
obs--98.83 %

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