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- PDB-9c9v: HBV capsid with compound 3i -

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Basic information

Entry
Database: PDB / ID: 9c9v
TitleHBV capsid with compound 3i
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / HBV capsid / assembly modulators
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsOlland, A.M. / Suto, R.K. / Fontano, E. / Colussi, T.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Rational Design, Synthesis, and Structure-Activity Relationship of a Novel Isoquinolinone-Based Series of HBV Capsid Assembly Modulators Leading to the Identification of Clinical Candidate AB-836.
Authors: Cole, A.G. / Kultgen, S.G. / Mani, N. / Fan, K.Y. / Ardzinski, A. / Stever, K. / Dorsey, B.D. / Mesaros, E.F. / Thi, E.P. / Graves, I. / Tang, S. / Harasym, T.O. / Lee, A.C.H. / Olland, A. / ...Authors: Cole, A.G. / Kultgen, S.G. / Mani, N. / Fan, K.Y. / Ardzinski, A. / Stever, K. / Dorsey, B.D. / Mesaros, E.F. / Thi, E.P. / Graves, I. / Tang, S. / Harasym, T.O. / Lee, A.C.H. / Olland, A. / Suto, R.K. / Sofia, M.J.
History
DepositionJun 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,83812
Polymers113,3436
Non-polymers2,4956
Water00
1
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6134
Polymers37,7812
Non-polymers8322
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-35 kcal/mol
Surface area13760 Å2
MethodPISA
2
C: Capsid protein
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6134
Polymers37,7812
Non-polymers8322
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-34 kcal/mol
Surface area13180 Å2
MethodPISA
3
E: Capsid protein
F: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6134
Polymers37,7812
Non-polymers8322
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-32 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.944, 87.919, 108.503
Angle α, β, γ (deg.)90, 102.748, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Capsid protein / Core antigen / Core protein / HBcAg / p21.5


Mass: 18890.510 Da / Num. of mol.: 6 / Mutation: Y132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7R9I1
#2: Chemical
ChemComp-A1AVK / N'-(3-chloro-4-fluorophenyl)-N-(2-methylpropyl)-N-[(1R)-1-(1-oxo-1,2-dihydroisoquinolin-4-yl)ethyl]urea


Mass: 415.888 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H23ClFN3O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.12 Å3/Da / Density % sol: 60.56 % / Description: large hexagonal crystals
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 3350, 10 to 14% (+/-)-2-methyl-2,4-pentanediol (MPD), 8 to 10% isopropanol, and 100 mM ammonium citrate/citric acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.97625 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 41271 / % possible obs: 98.7 % / Redundancy: 3.3 % / CC1/2: 0.937 / Net I/σ(I): 6.1
Reflection shellResolution: 2.63→2.72 Å / Num. unique obs: 3899 / CC1/2: 0.609

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→48.409 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.93 / SU B: 39.586 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / ESU R: 0.422 / ESU R Free: 0.282
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.258 2055 5.007 %
Rwork0.2239 38991 -
all0.226 --
obs-41046 98.611 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 72.001 Å2
Baniso -1Baniso -2Baniso -3
1--0.935 Å20 Å2-0.235 Å2
2---0.743 Å20 Å2
3---1.618 Å2
Refinement stepCycle: LAST / Resolution: 2.63→48.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 174 0 6409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126668
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166063
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.8489149
X-RAY DIFFRACTIONr_angle_other_deg0.6251.75413923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3125793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.683543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50410944
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.28610280
X-RAY DIFFRACTIONr_chiral_restr0.0750.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027858
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021608
X-RAY DIFFRACTIONr_nbd_refined0.2470.21768
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.25408
X-RAY DIFFRACTIONr_nbtor_refined0.1980.23326
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.23366
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2145
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1690.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.10.28
X-RAY DIFFRACTIONr_nbd_other0.1690.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0730.21
X-RAY DIFFRACTIONr_mcbond_it5.7426.1013187
X-RAY DIFFRACTIONr_mcbond_other5.7336.1023187
X-RAY DIFFRACTIONr_mcangle_it9.05610.9353975
X-RAY DIFFRACTIONr_mcangle_other9.05510.9363976
X-RAY DIFFRACTIONr_scbond_it5.296.0843481
X-RAY DIFFRACTIONr_scbond_other5.2896.0843481
X-RAY DIFFRACTIONr_scangle_it8.38811.1685174
X-RAY DIFFRACTIONr_scangle_other8.38711.1675175
X-RAY DIFFRACTIONr_lrange_it11.80557.6947956
X-RAY DIFFRACTIONr_lrange_other11.80457.6927957
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.63-2.6980.4261220.426850.40130290.850.85692.67080.377
2.698-2.7720.41390.37327040.37529850.8620.8895.24290.346
2.772-2.8520.3661490.32826660.3329150.890.91396.56950.298
2.852-2.9390.3381230.32626610.32728260.9090.91598.51380.3
2.939-3.0350.3661390.31625640.31927230.9030.92399.26550.3
3.035-3.1410.3181610.29724600.29926280.9330.93599.73360.281
3.141-3.2590.3111330.24724010.2525400.9330.95699.76380.231
3.259-3.3920.2741230.22823440.2324710.9510.96599.83810.216
3.392-3.5420.2661240.21322150.21623390.9510.9711000.206
3.542-3.7140.2551290.22521250.22722540.9530.9671000.23
3.714-3.9130.25950.20720420.20921380.9630.97299.95320.219
3.913-4.1490.245900.18419420.18720350.9570.97899.85260.198
4.149-4.4330.2880.16118060.16318960.9730.98399.89450.178
4.433-4.7850.181860.13917090.14118000.9780.98799.72220.157
4.785-5.2370.21790.17515730.17716530.9730.98399.93950.196
5.237-5.8460.223760.18114370.18415140.9720.98299.9340.205
5.846-6.7340.259590.19212510.19513120.9640.97899.84760.222
6.734-8.2080.237550.20510610.20711220.9670.97499.46520.242
8.208-11.4450.211570.1918350.1928940.970.97899.77630.258
11.445-48.4090.232280.3015100.2975380.9690.9431000.37
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)
12.6489-0.30570.28781.2006-0.44380.17610.0098-0.1261-0.21330.10120.02010.0607-0.0345-0.0165-0.02990.0105-0.00290.01950.0116-0.02260.2124155.4126-51.1709138.6474
22.9009-0.2616-0.02531.35560.42350.13470.1135-0.13630.2240.1651-0.0847-0.05450.0553-0.0324-0.02880.0333-0.02280.00680.02340.02270.1989177.6199-41.6958138.459
31.2663-0.74350.3693.22160.16620.16020.027-0.09780.010.0374-0.0063-0.15480.0156-0.0371-0.02070.0065-0.00080.02970.01040.02020.2267176.3167-9.9248137.5537
41.7061-0.4695-0.14632.8842-0.61140.1681-0.0001-0.0635-0.07080.12310.01690.2018-0.03060.0037-0.01680.00920.0053-0.01710.01-0.03080.2102156.7685.1464137.4883
51.57240.9685-0.38282.40440.32030.2646-0.0412-0.03930.20010.09370.10090.06150.04540.0483-0.05970.01580.0093-0.0420.0117-0.00010.2254130.4726-11.8163137.4555
61.67060.84010.33282.5627-0.22880.1398-0.0716-0.0701-0.15810.08820.1051-0.0847-0.0383-0.0406-0.03350.01940.01440.03190.0197-0.01390.2185126.8999-36.6293137.027
Refinement TLS groupSelection: ALL

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