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- PDB-5t2p: Hepatitis B virus core protein Y132A mutant in complex with sulfa... -

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Basic information

Entry
Database: PDB / ID: 5t2p
TitleHepatitis B virus core protein Y132A mutant in complex with sulfamoylbenzamide (SBA_R01)
ComponentsCore protein
KeywordsVIRAL PROTEIN / HEPATITIS B VIRUS / HBV / CORE PROTEIN / CAPSID / Y132A DIMER / Y132A HEXAMER / sulfamoylbenzamide / SBA_R01
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / host cell / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Hepatitis B viral capsid (hbcag) fold / Viral capsid, core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-K89 / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.693 Å
AuthorsZhou, Z. / Xu, Z.H.
CitationJournal: Sci Rep / Year: 2017
Title: Heteroaryldihydropyrimidine (HAP) and Sulfamoylbenzamide (SBA) Inhibit Hepatitis B Virus Replication by Different Molecular Mechanisms.
Authors: Zhou, Z. / Hu, T. / Zhou, X. / Wildum, S. / Garcia-Alcalde, F. / Xu, Z. / Wu, D. / Mao, Y. / Tian, X. / Zhou, Y. / Shen, F. / Zhang, Z. / Tang, G. / Najera, I. / Yang, G. / Shen, H.C. / Young, J.A. / Qin, N.
History
DepositionAug 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,72732
Polymers104,9216
Non-polymers3,80526
Water10,953608
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.927, 68.048, 85.703
Angle α, β, γ (deg.)68.490, 69.990, 83.490
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEU(chain A and (resseq 1:15 or (resid 16 and (name...AA1 - 151 - 15
12LEULEULEULEU(chain A and (resseq 1:15 or (resid 16 and (name...AA1616
13METMETGLNGLN(chain A and (resseq 1:15 or (resid 16 and (name...AA1 - 1551 - 155
14METMETGLNGLN(chain A and (resseq 1:15 or (resid 16 and (name...AA1 - 1551 - 155
15METMETGLNGLN(chain A and (resseq 1:15 or (resid 16 and (name...AA1 - 1551 - 155
16METMETGLNGLN(chain A and (resseq 1:15 or (resid 16 and (name...AA1 - 1551 - 155
17METMETGLNGLN(chain A and (resseq 1:15 or (resid 16 and (name...AA1 - 1551 - 155
18METMETGLNGLN(chain A and (resseq 1:15 or (resid 16 and (name...AA1 - 1551 - 155
21METMETLEULEU(chain B and (resseq 1:15 or (resid 16 and (name...BB1 - 151 - 15
22LEULEULEULEU(chain B and (resseq 1:15 or (resid 16 and (name...BB1616
23METMETGLNGLN(chain B and (resseq 1:15 or (resid 16 and (name...BB1 - 1551 - 155
24METMETGLNGLN(chain B and (resseq 1:15 or (resid 16 and (name...BB1 - 1551 - 155
25METMETGLNGLN(chain B and (resseq 1:15 or (resid 16 and (name...BB1 - 1551 - 155
26METMETGLNGLN(chain B and (resseq 1:15 or (resid 16 and (name...BB1 - 1551 - 155
27METMETGLNGLN(chain B and (resseq 1:15 or (resid 16 and (name...BB1 - 1551 - 155
28METMETGLNGLN(chain B and (resseq 1:15 or (resid 16 and (name...BB1 - 1551 - 155
31METMETLEULEU(chain C and (resseq 1:15 or (resid 16 and (name...CC1 - 151 - 15
32LEULEULEULEU(chain C and (resseq 1:15 or (resid 16 and (name...CC1616
33METMETTHRTHR(chain C and (resseq 1:15 or (resid 16 and (name...CC1 - 1421 - 142
34METMETTHRTHR(chain C and (resseq 1:15 or (resid 16 and (name...CC1 - 1421 - 142
35METMETTHRTHR(chain C and (resseq 1:15 or (resid 16 and (name...CC1 - 1421 - 142
36METMETTHRTHR(chain C and (resseq 1:15 or (resid 16 and (name...CC1 - 1421 - 142
37METMETTHRTHR(chain C and (resseq 1:15 or (resid 16 and (name...CC1 - 1421 - 142
38METMETTHRTHR(chain C and (resseq 1:15 or (resid 16 and (name...CC1 - 1421 - 142
41METMETLEULEU(chain D and (resseq 1:15 or (resid 16 and (name...DD1 - 151 - 15
42LEULEULEULEU(chain D and (resseq 1:15 or (resid 16 and (name...DD1616
43METMETGLNGLN(chain D and (resseq 1:15 or (resid 16 and (name...DD1 - 1551 - 155
44METMETGLNGLN(chain D and (resseq 1:15 or (resid 16 and (name...DD1 - 1551 - 155
45METMETGLNGLN(chain D and (resseq 1:15 or (resid 16 and (name...DD1 - 1551 - 155
46METMETGLNGLN(chain D and (resseq 1:15 or (resid 16 and (name...DD1 - 1551 - 155
47METMETGLNGLN(chain D and (resseq 1:15 or (resid 16 and (name...DD1 - 1551 - 155
48METMETGLNGLN(chain D and (resseq 1:15 or (resid 16 and (name...DD1 - 1551 - 155
51METMETLEULEU(chain F and (resseq 1:15 or (resid 16 and (name...FF1 - 151 - 15
52LEULEULEULEU(chain F and (resseq 1:15 or (resid 16 and (name...FF1616
53METMETGLNGLN(chain F and (resseq 1:15 or (resid 16 and (name...FF1 - 1551 - 155
54METMETGLNGLN(chain F and (resseq 1:15 or (resid 16 and (name...FF1 - 1551 - 155
55METMETGLNGLN(chain F and (resseq 1:15 or (resid 16 and (name...FF1 - 1551 - 155
56METMETGLNGLN(chain F and (resseq 1:15 or (resid 16 and (name...FF1 - 1551 - 155
57METMETGLNGLN(chain F and (resseq 1:15 or (resid 16 and (name...FF1 - 1551 - 155
58METMETGLNGLN(chain F and (resseq 1:15 or (resid 16 and (name...FF1 - 1551 - 155

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Core protein


Mass: 17486.916 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1-149 / Mutation: Y132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Production host: Escherichia coli (E. coli) / References: UniProt: L7R9I1

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Non-polymers , 6 types, 634 molecules

#2: Chemical
ChemComp-K89 / 4-fluoranyl-3-(4-oxidanylpiperidin-1-yl)sulfonyl-~{N}-[3,4,5-tris(fluoranyl)phenyl]benzamide


Mass: 432.389 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H16F4N2O4S
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 3.11 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 MM CITRATE, 21%(V/V) ISOPROPANOL, 1% (W/V) PEG 10000, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 134045 / % possible obs: 95.9 % / Redundancy: 4 % / Biso Wilson estimate: 26.41 Å2 / Rmerge(I) obs: 0.087 / Net I/av σ(I): 17.153 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.7-1.733.41.2190.498190.7
1.73-1.763.51.2030.534193.3
1.76-1.793.61.0880.599194.9
1.79-1.833.80.9210.719195.4
1.83-1.873.90.8080.789195.7
1.87-1.9140.7230.824195.7
1.91-1.964.10.6040.876195.9
1.96-2.024.10.4850.897195.8
2.02-2.074.10.3750.941196.2
2.07-2.144.20.290.966196.3
2.14-2.224.20.2250.98196.4
2.22-2.314.20.1830.982196.5
2.31-2.414.20.1460.988196.7
2.41-2.544.20.1310.989196.8
2.54-2.74.20.1040.992197
2.7-2.914.20.0850.994197
2.91-3.24.10.0720.995197.1
3.2-3.664.10.0580.995196.8
3.66-4.614.10.0480.995195.2
4.61-504.10.0410.996197.7

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMG

4bmg


Resolution: 1.693→39.043 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.89
RfactorNum. reflection% reflection
Rfree0.2079 3214 2.4 %
Rwork0.1795 --
obs0.1802 133954 95.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.08 Å2 / Biso mean: 40.2635 Å2 / Biso min: 18.53 Å2
Refinement stepCycle: final / Resolution: 1.693→39.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7159 0 245 608 8012
Biso mean--37.64 47.15 -
Num. residues----898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017775
X-RAY DIFFRACTIONf_angle_d0.95210692
X-RAY DIFFRACTIONf_chiral_restr0.0511183
X-RAY DIFFRACTIONf_plane_restr0.0081351
X-RAY DIFFRACTIONf_dihedral_angle_d18.3194522
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2583X-RAY DIFFRACTION7.662TORSIONAL
12B2583X-RAY DIFFRACTION7.662TORSIONAL
13C2583X-RAY DIFFRACTION7.662TORSIONAL
14D2583X-RAY DIFFRACTION7.662TORSIONAL
15F2583X-RAY DIFFRACTION7.662TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6933-1.71860.3327980.34344742484079
1.7186-1.74540.33051230.33075498562193
1.7454-1.7740.28791650.31895588575394
1.774-1.80460.28851310.28965657578895
1.8046-1.83740.26111340.27275755588996
1.8374-1.87280.29441440.25515667581195
1.8728-1.9110.26951440.24715720586496
1.911-1.95260.26221260.23455771589796
1.9526-1.9980.27881370.22825727586496
1.998-2.04790.28831400.21595716585696
2.0479-2.10330.24011450.20755660580596
2.1033-2.16520.23211440.18575757590196
2.1652-2.23510.21511400.17835812595297
2.2351-2.31490.20941470.16985774592197
2.3149-2.40760.19771450.16965711585697
2.4076-2.51720.21861400.18055814595497
2.5172-2.64990.18871390.17585760589997
2.6499-2.81580.22911490.17715774592397
2.8158-3.03320.18891560.18085779593597
3.0332-3.33830.22481330.17475778591197
3.3383-3.8210.17731420.15745773591597
3.821-4.81260.16161470.13765683583096
4.8126-39.05330.18731450.16025824596997
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)
10.6418-0.5425-0.6886-0.35160.03691.2831-0.1674-0.0946-0.07870.08710.070.0845-0.0209-0.0152-0.00060.286-0.0010.03860.2359-0.00290.250416.395726.1904-13.8856
2-0.1607-0.1389-0.17860.74470.46480.75840.0152-0.0151-0.0001-0.017-0.06970.00230.04410.0332-00.1893-0.02380.00460.2187-0.01820.224227.733614.9824-35.8057
30.042-0.270.08910.33110.07310.6940.0474-0.00370.0523-0.0008-0.0343-0.0714-0.03650.030800.222-0.01350.00860.2330.02220.2286-8.880459.7514-36.2258
40.9869-0.79360.04550.3034-0.08381.9361-0.0268-0.02910.12330.00140.0151-0.06330.23720.19720.00010.2860.0126-0.01130.21750.00390.2159-2.5350.9375-13.797
50.9824-0.9950.0981.3888-0.9271.3720.09070.01510.0254-0.0254-0.0748-0.02360.06480.1805-0.00110.20570.0233-0.03070.2196-0.02140.197820.921231.8002-60.7338
60.3275-0.38960.29430.04980.08890.67370.04150.0364-0.0084-0.0044-0.0125-0.013-0.0899-0.001800.22350.01560.00320.21870.02230.23892.521650.3298-64.3136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A1 - 155
2X-RAY DIFFRACTION2chain 'B'B1 - 155
3X-RAY DIFFRACTION3chain 'E'E1 - 155
4X-RAY DIFFRACTION4chain 'F'F1 - 155
5X-RAY DIFFRACTION5chain 'C'C1 - 142
6X-RAY DIFFRACTION6chain 'D'D1 - 155

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