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- PDB-7k5m: CRYSTAL STRUCTURE OF HBV CAPSID Y132A MUTANT IN COMPLEX WITH N-(3... -

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Basic information

Entry
Database: PDB / ID: 7k5m
TitleCRYSTAL STRUCTURE OF HBV CAPSID Y132A MUTANT IN COMPLEX WITH N-(3-chloro-4-fluorophenyl)-3-phenyl-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide AT 2.65A RESOLUTION
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / HVB 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 / identical protein binding
Similarity search - Function
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-VXJ / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus genotype D subtype adw
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKuduk, S.D. / Stoops, B. / Alexander, R. / Lam, A.M. / Espiritu, C. / Vogel, R. / Lau, V. / Klumpp, K. / Flores, O.A. / Hartman, G.D. ...Kuduk, S.D. / Stoops, B. / Alexander, R. / Lam, A.M. / Espiritu, C. / Vogel, R. / Lau, V. / Klumpp, K. / Flores, O.A. / Hartman, G.D. / Lukacs, C.M. / Abendroth, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: Identification of a new class of HBV capsid assembly modulator.
Authors: Kuduk, S.D. / Stoops, B. / Alexander, R. / Lam, A.M. / Espiritu, C. / Vogel, R. / Lau, V. / Klumpp, K. / Flores, O.A. / Hartman, G.D.
History
DepositionSep 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 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)109,42317
Polymers106,8986
Non-polymers2,52511
Water543
1
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4946
Polymers35,6332
Non-polymers8624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-27 kcal/mol
Surface area13560 Å2
MethodPISA
2
C: Capsid protein
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4345
Polymers35,6332
Non-polymers8023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-29 kcal/mol
Surface area13390 Å2
MethodPISA
3
E: Capsid protein
F: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4946
Polymers35,6332
Non-polymers8624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-20 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.580, 87.960, 106.710
Angle α, β, γ (deg.)90.000, 103.530, 90.000
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: 17816.332 Da / Num. of mol.: 6 / Mutation: Y132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979)
Strain: isolate United Kingdom/adyw/1979 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03147
#2: Chemical
ChemComp-VXJ / N-(3-chloro-4-fluorophenyl)-3-phenyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide


Mass: 370.808 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H16ClFN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M ammonium citrate/citric acid pH 6.5, 9% isopropanol, 10% PEG 3350, 10% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.65→48.035 Å / Num. obs: 37097 / % possible obs: 93.2 % / Redundancy: 2.93 % / Biso Wilson estimate: 42.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.091 / Χ2: 1.006 / Net I/σ(I): 10.37 / Num. measured all: 108596 / Scaling rejects: 10
Reflection shellResolution: 2.65→48.035 Å / Redundancy: 2.87 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 1234 / Num. possible: 486 / Num. unique obs: 421 / CC1/2: 0.999 / Rrim(I) all: 0.024 / % possible all: 95.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev-1932refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal model

Resolution: 2.65→48.035 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 1979 5.35 %0
Rwork0.2424 34990 --
obs0.2442 36969 92.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.32 Å2 / Biso mean: 75.6629 Å2 / Biso min: 40.02 Å2
Refinement stepCycle: final / Resolution: 2.65→48.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6028 0 176 3 6207
Biso mean--68.7 61.09 -
Num. residues----785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036417
X-RAY DIFFRACTIONf_angle_d0.6838800
X-RAY DIFFRACTIONf_chiral_restr0.032971
X-RAY DIFFRACTIONf_plane_restr0.0041106
X-RAY DIFFRACTIONf_dihedral_angle_d11.3492162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.65-2.71620.4741520.4371251595
2.7162-2.78960.36921310.377254395
2.7896-2.87170.34791380.3709248993
2.8717-2.96440.43361460.3633249993
2.9644-3.07030.40131300.3458249994
3.0703-3.19320.35671390.3209252794
3.1932-3.33850.29451440.2644252894
3.3385-3.51450.28091490.228251794
3.5145-3.73460.27021430.221248493
3.7346-4.02280.24371470.2115246092
4.0228-4.42740.21541220.1811251892
4.4274-5.06740.19891490.1788247092
5.0674-6.3820.2431560.216245891
6.382-480.22711330.1916248389
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)
13.03980.3269-0.43644.0769-2.00262.3743-0.1013-0.1107-0.00530.3363-0.04430.343-0.1749-0.0124-0.00330.6765-0.02750.0120.6868-0.07130.2658-43.6271-12.281630.308
23.12320.88530.41223.41490.48893.59290.94760.2214-0.30980.09140.9851-0.1279-0.29920.7992.80550.697-0.050.05050.83810.253-1.3855-53.5578-11.702430.5797
30.4680.10590.36460.22240.06410.2943-0.55360.9308-1.0572-0.12220.03940.1040.5765-0.6604-0.00170.8071-0.09410.01230.64460.05541.1143-70.4428-15.93827.2845
41.12890.45850.3921.16831.4682.1495-0.0915-0.05220.30530.03420.0308-0.17380.1671-0.0102-00.6645-0.0394-0.03750.7610.01410.8378-27.0286-4.137429.0347
54.35550.5193-0.35495.50070.96570.33450.1405-0.25860.35680.346-0.28790.22640.03140.028900.6642-0.0398-0.01750.70740.01970.6938-33.2789-2.266432.3181
60.55940.5199-0.52270.9244-0.75420.567-0.1760.52991.0934-0.23020.1217-0.3431-0.1436-0.02290.00040.6955-0.0127-0.03010.7344-0.0371.3072-10.6154-2.191925.2795
74.10950.36791.04254.2728-0.2621.380.09620.023-0.29760.1187-0.2299-0.06650.0303-0.0182-0.00010.60140.03670.03780.69830.10710.9771-30.748133.721329.7777
80.0112-0.00590.02310.0055-0.00510.0445-0.3289-2.1362-0.34611.22620.4855-0.2515-0.5026-0.1702-0.00071.15270.0997-0.11121.38110.18481.0558-30.921532.392347.7466
90.9449-0.1776-0.10811.3293-0.42421.59910.0830.2818-0.101-0.18410.0348-0.9259-0.1085-0.0722-00.67040.00870.0230.6765-0.08261.1223-22.572720.415326.9078
101.2552-0.6436-0.63571.4227-0.36232.0777-0.0355-0.15550.0287-0.00930.0958-0.09010.0170.04550.00010.69880.0620.01030.6826-0.06991.0062-46.441543.738428.7469
112.93720.1950.06633.97310.45270.32410.1309-0.1802-0.35620.2095-0.13760.06830.6766-0.3503-00.71550.0085-0.01540.7084-0.04490.9995-42.699933.117331.8944
122.40720.8876-1.03681.7485-0.22370.4357-0.0407-0.1801-0.340.1486-0.03940.3573-0.33870.449900.72290.0468-0.00010.7541-0.08820.6032-47.680544.059732.1931
130.98990.09340.8580.5744-0.16950.79590.21070.2645-0.2461-0.2128-0.39441.12230.2185-0.0243-0.00010.7283-0.00760.06610.69880.1141.1858-56.066657.795925.2769
140.93590.5126-1.06881.73860.36691.76980.1498-0.1540.2135-0.07060.0791-0.5110.03570.113900.7404-0.0243-0.1260.65950.02930.9425-73.624225.615228.9473
152.7405-0.61550.28823.11820.59340.32660.043-0.1933-0.5026-0.24980.33050.5499-0.0682-0.3349-0.00020.73220.0218-0.04050.7255-0.02270.5513-81.177417.13128.9976
160.9565-0.2001-0.4771.60610.52440.6660.0541-0.13480.19260.2610.15730.12010.55480.29840.94510.962-0.0565-0.00140.72060.0491-0.6833-74.100726.851630.5617
170.6614-0.18980.32131.2296-0.93870.672-0.19130.05130.7988-0.5263-0.10350.72480.1056-0.22810.00020.712-0.03260.0970.69790.03151.4594-66.742940.90325.055
183.31170.0814-0.0124.5087-0.88232.6364-0.1342-0.2637-0.0475-0.02470.134-0.4594-0.1819-0.02740.00010.71190.02840.07120.6450.00350.598-74.52277.096830.2055
193.756-0.67250.07982.8629-1.95311.3566-0.06620.34-1.3753-0.03550.5491-0.0419-0.12720.01220.13310.7805-0.03430.04160.72930.06080.0067-81.5346-5.666628.7008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth seq-ID
1X-RAY DIFFRACTION10
2X-RAY DIFFRACTION20
3X-RAY DIFFRACTION30
4X-RAY DIFFRACTION40
5X-RAY DIFFRACTION50
6X-RAY DIFFRACTION60
7X-RAY DIFFRACTION70
8X-RAY DIFFRACTION80
9X-RAY DIFFRACTION90
10X-RAY DIFFRACTION100
11X-RAY DIFFRACTION110
12X-RAY DIFFRACTION120
13X-RAY DIFFRACTION130
14X-RAY DIFFRACTION140
15X-RAY DIFFRACTION150
16X-RAY DIFFRACTION160
17X-RAY DIFFRACTION170
18X-RAY DIFFRACTION180
19X-RAY DIFFRACTION190

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