3DLR: Catalytic core domain from PFV integrase

Crystal structure of the catalytic core domain from PFV integrase. Determined by X-ray diffraction at 2.2 Å resolution. Released 9 Dec 2008.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Human spumaretrovirus
Chains: 1
Atoms: 1,290
Mol. weight: 22.67 kDa
Ligands: MG
Released: 9 Dec 2008

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

Secondary structure: helices and β-sheets

3DLR contains 9 α-helices and 7 β-strands across 1 chain. 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: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	124-130	7	1
β-strand	136	1	2
β-strand	139	1	2
β-strand	141-147	7	1
β-strand	153-158	6	1
α-helix	163-173	11
β-strand	181-184	4	1
α-helix	188-191	4
α-helix	193-202	10
α-helix	204	1
β-strand	205-208	4	1
α-helix	221-235	15
α-helix	239-241	3
α-helix	242-254	13
α-helix	265-269	5
α-helix	294-303	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrase	A	protein	202	Human spumaretrovirus	P14350

Sequence of entity 1 (A), FASTA

>3DLR_1 Integrase (chains A)
GPGSGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSA
TVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNS
DIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLD
LTREEELSLLQEIRTSLYHPST

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Functional and structural characterization of the integrase from the prototype foamy virus. Valkov, E., Gupta, S.S., Hare, S. et al. Nucleic Acids Res (2009) 37:243-255. DOI 10.1093/nar/gkn938 · PubMed

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

2X78 2.0 Å, Human foamy virus integrase - catalytic core.
3OYM 2.02 Å, Crystal structure of the PFV N224H mutant intasome bound to manganese
2X6N 2.06 Å, Human foamy virus integrase - catalytic core. Manganese-bound structure.
2X6S 2.29 Å, Human foamy virus integrase - catalytic core. Magnesium-bound structure.
2X74 2.34 Å, Human foamy virus integrase - catalytic core.
4BE2 2.38 Å, PFV intasome with inhibitor XZ-259
3S3M 2.49 Å, Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium…
3S3N 2.49 Å, Crystal structure of the Prototype Foamy Virus (PFV) S217H mutant intasome in complex…
3OYF 2.51 Å, Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium…
4BDY 2.52 Å, PFV intasome with inhibitor XZ-89
4E7I 2.53 Å, PFV intasome freeze-trapped prior to 3'-processing, Mn-bound form (UI-Mn)
3OYB 2.54 Å, Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium…

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