3S3M: Prototype Foamy Virus (PFV) intasome

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and Dolutegravir (S/GSK1349572). Determined by X-ray diffraction at 2.49 Å resolution. Released 13 Jul 2011.

Method
X-ray diffraction
Resolution
2.49 Å
Organism
Human spumaretrovirus
Chains
4
Atoms
5,424
Mol. weight
101.17 kDa
Ligands
ZN, MG, DLU, HEZ
Released
13 Jul 2011

Explore 3S3M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3S3M contains 36 α-helices and 31 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 25 helices, 22 β-strands

ElementResiduesLengthSheet
α-helix9-168
β-strand30-3341
β-strand36-4161
β-strand44-4741
α-helix51-6313
α-helix69-779
β-strand8011
α-helix85-939
α-helix97-1026
α-helix104-1052
β-strand108-10922
α-helix110-1134
α-helix115-1184
β-strand124-13073
β-strand13614
β-strand13914
β-strand141-14773
β-strand153-15863
α-helix163-17412
β-strand181-18443
α-helix188-1914
α-helix193-2008
α-helix2041
β-strand205-20843
α-helix209-2102
α-helix214-2174
α-helix218-23518
α-helix243-2453
α-helix246-2549
β-strand25815
β-strand26315
α-helix265-2706
α-helix288-30013
α-helix308-3114
β-strand314-31522
β-strand322-32546
β-strand32617
α-helix3271
α-helix330-3312
β-strand33717
α-helix338-3403
β-strand341-34886
β-strand351-35556
β-strand361-36556
α-helix366-3683
β-strand369-37136
α-helix3721
Chain B: 11 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix117-1193
β-strand124-13078
β-strand13619
β-strand13919
β-strand141-14778
β-strand153-15868
α-helix163-17311
β-strand181-18448
α-helix188-1914
α-helix193-2019
α-helix2041
β-strand205-20848
α-helix2091
β-strand210110
β-strand213110
α-helix218-23417
α-helix242-25413
α-helix265-2706
α-helix286-2872
α-helix288-29710

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
PFV integraseA, Bprotein395Human spumaretrovirusP14350
5'-d(*ap*tp*tp*gp*tp*cp*ap*tp*gp*gp*ap*ap*tp*tp*tp*cp*gp*cp*a)-3'CDNA19
5'-d(*tp*gp*cp*gp*ap*ap*ap*tp*tp*cp*cp*ap*tp*gp*ap*cp*a)-3'DDNA17
Sequence of entity 1 (A, B), FASTA
>3S3M_1 PFV integrase (chains A, B)
GPGCNTKKPNLDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKI
VLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDR
PQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIA
IPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVG
RPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQE
IRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDH
LGNNRTVSIDNLKPTSHQNGTTNDTATMDHLEKNE
Sequence of entity 2 (C), FASTA
>3S3M_2 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3' (chains C)
ATTGTCATGGAATTTCGCA
Sequence of entity 3 (D), FASTA
>3S3M_3 5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3' (chains D)
TGCGAAATTCCATGACA

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1
MGMagnesium ionMg2
DLU(4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-he…C20 H19 F2 N3 O51
HEZHexane-1,6-diolC6 H14 O21

Water and common crystallization additives (SO4, GOL, NH4) are not listed.

Primary citation

Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572). Hare, S., Smith, S.J., Metifiot, M. et al. Mol Pharmacol (2011) 80:565-572. DOI 10.1124/mol.111.073189 · PubMed

Other PDB entries of the same protein (UniProt P14350), best resolution first:

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