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- PDB-9pgu: HIV Capsid Hexamer bound to Compound 40 -

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Basic information

Entry
Database: PDB / ID: 9pgu
TitleHIV Capsid Hexamer bound to Compound 40
ComponentsHIV-1 capsid
KeywordsVIRAL PROTEIN / Capsid / p24 / HIV-1
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / virion membrane / structural molecule activity / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å
AuthorsSomoza, J.R. / Anderson, R.L. / Villasenor, A.G. / Ferrao, R.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of Lenacapavir: First-in-Class Twice-Yearly Capsid Inhibitor for HIV-1 Treatment and Pre-exposure Prophylaxis
Authors: Canales, E. / Tse, W. / Schroeder, S.D. / Chou, C.H. / Liu, Q. / Zhang, J. / Lazerwith, S.E. / Morganelli, P. / Saito, R.D. / Brizgys, G. / Li, J. / Wu, Q. / Graupe, M. / Halcomb, R.L. / ...Authors: Canales, E. / Tse, W. / Schroeder, S.D. / Chou, C.H. / Liu, Q. / Zhang, J. / Lazerwith, S.E. / Morganelli, P. / Saito, R.D. / Brizgys, G. / Li, J. / Wu, Q. / Graupe, M. / Halcomb, R.L. / Desai, M. / Cannizzaro, C. / Hu, E. / Perry, J.K. / Villasenor, A.G. / Somoza, J.R. / Ferrao, R.D. / Swaminathan, S. / Zheng, J. / Lu, B. / Mwangi, J. / Wang, K. / Subramanian, R. / Smith, B.J. / Rhodes, G. / Rowe, W. / Sauer, D. / Lad, L. / Papalia, G.A. / Clancy, S. / Stepan, G.J. / Yu, H. / Sakowicz, R. / Shi, B. / Carr, G. / Bam, R.A. / Tsai, L.K. / Singer, E. / Hansen, D. / Mulato, A. / Yant, S.R. / Cihlar, T. / Link, J.O.
History
DepositionJul 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 capsid
B: HIV-1 capsid
C: HIV-1 capsid
D: HIV-1 capsid
E: HIV-1 capsid
F: HIV-1 capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,36812
Polymers153,5556
Non-polymers3,8136
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint-109 kcal/mol
Surface area56110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.650, 134.650, 211.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
HIV-1 capsid


Mass: 25592.469 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: B6DRA0
#2: Chemical
ChemComp-A1CH6 / (5M)-5-{2-[(1S)-2-(3,5-difluorophenyl)-1-{2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamido}ethyl]pyridin-3-yl}-2-fluorobenzamide


Mass: 635.507 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C30H21F8N5O2 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 7% peg 8000, 0.1M sodium malonate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 3.36→49.28 Å / Num. obs: 52800 / % possible obs: 99.91 % / Redundancy: 7 % / Biso Wilson estimate: 102.16 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.09069 / Net I/σ(I): 7.92
Reflection shellResolution: 3.36→3.45 Å / Num. unique obs: 3744 / CC1/2: 0.265

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.36→49.28 Å / SU ML: 0.503 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9573
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2623 1999 7.05 %
Rwork0.2209 26349 -
obs0.2238 28348 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.17 Å2
Refinement stepCycle: LAST / Resolution: 3.36→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9495 0 270 0 9765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00279993
X-RAY DIFFRACTIONf_angle_d0.499413654
X-RAY DIFFRACTIONf_chiral_restr0.03681529
X-RAY DIFFRACTIONf_plane_restr0.00421748
X-RAY DIFFRACTIONf_dihedral_angle_d11.75323674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.36-3.450.41071390.34121827X-RAY DIFFRACTION99.34
3.45-3.540.36911410.28961860X-RAY DIFFRACTION99.9
3.54-3.650.35651390.2831845X-RAY DIFFRACTION100
3.65-3.760.33031400.28281837X-RAY DIFFRACTION100
3.76-3.90.31991400.26731851X-RAY DIFFRACTION100
3.9-4.050.30741410.22921863X-RAY DIFFRACTION100
4.05-4.240.29931420.21671867X-RAY DIFFRACTION100
4.24-4.460.24391410.20791849X-RAY DIFFRACTION100
4.46-4.740.2511430.20721882X-RAY DIFFRACTION100
4.74-5.110.26891430.19211881X-RAY DIFFRACTION99.95
5.11-5.620.28851430.21321888X-RAY DIFFRACTION100
5.62-6.430.26481450.22331915X-RAY DIFFRACTION100
6.43-8.090.21831460.20171931X-RAY DIFFRACTION100
8.1-49.280.19271560.19242053X-RAY DIFFRACTION99.55

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