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- PDB-7s76: HBV CAPSID Y132A WITH COMPOUND 10b AT 2.5A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 7s76
TitleHBV CAPSID Y132A WITH COMPOUND 10b AT 2.5A RESOLUTION
ComponentsCapsid protein
KeywordsVIRAL PROTEIN/INHIBITOR / core / VIRAL PROTEIN / inhibitor / VIRAL PROTEIN-INHIBITOR complex
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-8EI / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus genotype A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOlland, A.M. / Suto, R.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Med Chem / Year: 2022
Title: The identification of highly efficacious functionalised tetrahydrocyclopenta[ c ]pyrroles as inhibitors of HBV viral replication through modulation of HBV capsid assembly.
Authors: Cole, A.G. / Kultgen, S.G. / Mani, N. / Ardzinski, A. / Fan, K.Y. / Thi, E.P. / Dorsey, B.D. / Stever, K. / Chiu, T. / Tang, S. / Daly, O. / Phelps, J.R. / Harasym, T. / Olland, A. / Suto, R.K. / Sofia, M.J.
History
DepositionSep 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)110,70912
Polymers108,0276
Non-polymers2,6816
Water00
1
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9034
Polymers36,0092
Non-polymers8942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-35 kcal/mol
Surface area14070 Å2
MethodPISA
2
C: Capsid protein
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9034
Polymers36,0092
Non-polymers8942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-35 kcal/mol
Surface area13210 Å2
MethodPISA
3
E: Capsid protein
F: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9034
Polymers36,0092
Non-polymers8942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-29 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.239, 88.306, 103.712
Angle α, β, γ (deg.)90.000, 103.890, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA0 - 1433 - 146
21SERSERLEULEUBB0 - 1433 - 146
12SERSERTHRTHRAA0 - 1423 - 145
22SERSERTHRTHRCC0 - 1423 - 145
13METMETTHRTHRAA1 - 1424 - 145
23METMETTHRTHRDD1 - 1424 - 145
14SERSERTHRTHRAA0 - 1423 - 145
24SERSERTHRTHREE0 - 1423 - 145
15SERSERTHRTHRAA0 - 1423 - 145
25SERSERTHRTHRFF0 - 1423 - 145
16SERSERTHRTHRBB0 - 1423 - 145
26SERSERTHRTHRCC0 - 1423 - 145
17METMETTHRTHRBB1 - 1424 - 145
27METMETTHRTHRDD1 - 1424 - 145
18SERSERTHRTHRBB0 - 1423 - 145
28SERSERTHRTHREE0 - 1423 - 145
19SERSERTHRTHRBB0 - 1423 - 145
29SERSERTHRTHRFF0 - 1423 - 145
110METMETTHRTHRCC1 - 1424 - 145
210METMETTHRTHRDD1 - 1424 - 145
111SERSERTHRTHRCC0 - 1423 - 145
211SERSERTHRTHREE0 - 1423 - 145
112SERSERTHRTHRCC0 - 1423 - 145
212SERSERTHRTHRFF0 - 1423 - 145
113METMETTHRTHRDD1 - 1424 - 145
213METMETTHRTHREE1 - 1424 - 145
114METMETTHRTHRDD1 - 1424 - 145
214METMETTHRTHRFF1 - 1424 - 145
115SERSERTHRTHREE0 - 1423 - 145
215SERSERTHRTHRFF0 - 1423 - 145

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 18004.578 Da / Num. of mol.: 6 / Mutation: Y132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus genotype A / Production host: Escherichia coli (E. coli) / References: UniProt: L7R9I1
#2: Chemical
ChemComp-8EI / (1-methyl-1H-1,2,4-triazol-3-yl)methyl {(4S)-1-[(3-chloro-4-fluorophenyl)carbamoyl]-2-methyl-2,4,5,6-tetrahydrocyclopenta[c]pyrrol-4-yl}carbamate


Mass: 446.863 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H20ClFN6O3
Has ligand of interestY

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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: 3.14 Å3/Da / Density % sol: 60.89 % / Description: hexagonal plates
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 3350, 10 to 14% (+/-)-2-methyl-2,4-pentanediol (MPD), 8 to 10% isopropanol, and 100 mM ammonium citrate/citric acid

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 46072 / % possible obs: 99.4 % / Redundancy: 3.33 % / CC1/2: 0.99 / Net I/σ(I): 5.4
Reflection shellResolution: 2.5→2.65 Å / Mean I/σ(I) obs: 1.06 / Num. unique obs: 7351 / CC1/2: 0.742 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E0I

5e0i


Resolution: 2.5→47.26 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.899 / SU B: 25.264 / SU ML: 0.453 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.413 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2975 2307 5 %RANDOM
Rwork0.2696 ---
obs0.271 43745 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 238.45 Å2 / Biso mean: 67.483 Å2 / Biso min: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1--7.38 Å2-0 Å22.21 Å2
2---7.75 Å20 Å2
3---12.51 Å2
Refinement stepCycle: final / Resolution: 2.5→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6280 0 186 0 6466
Biso mean--90.31 --
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136677
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176055
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.6819164
X-RAY DIFFRACTIONr_angle_other_deg1.1521.5913951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2275788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63320.825303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.29615944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5981540
X-RAY DIFFRACTIONr_chiral_restr0.0520.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027366
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021508
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43700.05
12B43700.05
21A42690.06
22C42690.06
31A42280.06
32D42280.06
41A42060.06
42E42060.06
51A40470.06
52F40470.06
61B42880.04
62C42880.04
71B42400.06
72D42400.06
81B42090.06
82E42090.06
91B40560.04
92F40560.04
101C41900.06
102D41900.06
111C41990.06
112E41990.06
121C40760.05
122F40760.05
131D41460.07
132E41460.07
141D40130.04
142F40130.04
151E40470.05
152F40470.05
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.499 173 -
Rwork0.503 3163 -
all-3336 -
obs--97.8 %

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