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- PDB-8gbu: Hepatitis B capsid Y132A mutant with compound AB-506 -

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Basic information

Entry
Database: PDB / ID: 8gbu
TitleHepatitis B capsid Y132A mutant with compound AB-506
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Hepatitis B / Y132A / capsid
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
Chem-YWE / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHoranyi, P.S. / Mayclin, S.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: Design, synthesis, and structure-activity relationship of a bicyclic HBV capsid assembly modulator chemotype leading to the identification of clinical candidate AB-506.
Authors: Cole, A.G. / Kultgen, S.G. / Mani, N. / Quintero, J.G. / Yi Fan, K. / Ardzinski, A. / Stever, K. / Dorsey, B.D. / Phelps, J.R. / Lee, A.C.H. / Thi, E.P. / Chiu, T. / Tang, S. / Horanyi, P.S. ...Authors: Cole, A.G. / Kultgen, S.G. / Mani, N. / Quintero, J.G. / Yi Fan, K. / Ardzinski, A. / Stever, K. / Dorsey, B.D. / Phelps, J.R. / Lee, A.C.H. / Thi, E.P. / Chiu, T. / Tang, S. / Horanyi, P.S. / Mayclin, S.J. / Harasym, T.O. / Sofia, M.J.
History
DepositionFeb 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 9, 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)116,61120
Polymers113,3436
Non-polymers3,26814
Water1,33374
1
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2296
Polymers37,7812
Non-polymers1,4484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-27 kcal/mol
Surface area14200 Å2
MethodPISA
2
C: Capsid protein
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4296
Polymers37,7812
Non-polymers6484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-22 kcal/mol
Surface area14080 Å2
MethodPISA
3
E: Capsid protein
F: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9538
Polymers37,7812
Non-polymers1,1726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-21 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.936, 87.879, 100.827
Angle α, β, γ (deg.)90.00, 104.12, 90.00
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Production host: Escherichia coli (E. coli) / References: UniProt: L7R9I1
#2: Chemical
ChemComp-YWE / (1-methyl-1H-1,2,4-triazol-3-yl)methyl {(1S)-4-[(3-chloro-4-fluorophenyl)carbamoyl]-7-fluoro-2,3-dihydro-1H-inden-1-yl}carbamate


Mass: 461.849 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H18ClF2N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 2.88 Å3/Da / Density % sol: 57.29 % / Description: hexagonal
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM ammonium citrate/citric acid pH 6.5, 9%(vol/vol) isopropanol, 10%(wt/vol) PEG 3350, 10% (vol/vol) 2-Methyl-2,4-pentanediol, 0.6:0.3ul at a 2:1 volume ratio at 16C.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.5→97.78 Å / Num. obs: 44273 / % possible obs: 99 % / Redundancy: 3.77 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.072 / Net I/σ(I): 12.78
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.5-2.560.26332260.9840.3061
2.56-2.640.21431870.9860.251
2.64-2.710.20430960.9860.2361
2.71-2.80.16729860.9890.1941
2.8-2.890.14629090.9940.1681
2.89-2.990.13428140.9940.1551
2.99-3.10.10827490.9960.1241
3.1-3.230.09226110.9960.1071
3.23-3.370.06725300.9980.0791
3.37-3.540.06624000.9980.0761
3.54-3.730.05522970.9970.0641
3.73-3.950.04821740.9990.0561
3.95-4.230.04720430.9980.0541
4.23-4.560.04318890.9980.051
4.56-50.04317050.9970.0511
5-5.590.04416040.9980.0511
5.59-6.450.04314110.9980.051
6.45-7.910.03812180.9980.0451
7.91-11.180.0299050.9990.0341

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→97.78 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 27.444 / SU ML: 0.478 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2177 4.9 %RANDOM
Rwork0.233 ---
obs0.235 44273 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.2 Å2
Baniso -1Baniso -2Baniso -3
1--9.81 Å20 Å23.89 Å2
2---11.6 Å20 Å2
3---17.27 Å2
Refinement stepCycle: LAST / Resolution: 2.5→97.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 224 74 6916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197131
X-RAY DIFFRACTIONr_bond_other_d0.0020.026406
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9979787
X-RAY DIFFRACTIONr_angle_other_deg1.017314765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6045851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4922.563277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54315994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7341543
X-RAY DIFFRACTIONr_chiral_restr0.0750.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217849
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021536
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8478.0113413
X-RAY DIFFRACTIONr_mcbond_other4.8468.013412
X-RAY DIFFRACTIONr_mcangle_it7.62811.9774261
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 149 -
Rwork0.43 3070 -
obs--99.08 %

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