4BDY: PFV intasome with inhibitor XZ-89

PFV intasome with inhibitor XZ-89. Determined by X-ray diffraction at 2.52 Å resolution. Released 31 Oct 2012.

Method: X-ray diffraction
Resolution: 2.52 Å
Organism: HUMAN SPUMARETROVIRUS
Chains: 4
Atoms: 5,451
Mol. weight: 101.13 kDa
Ligands: CIJ, MG, ZN
Released: 31 Oct 2012

Explore 4BDY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BDY contains 37 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: 26 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	9-16	8
β-strand	32-33	2	1
β-strand	36-37	2	1
β-strand	38-41	4	2
β-strand	44-47	4	2
α-helix	51-65	15
α-helix	69-79	11
β-strand	80	1	2
α-helix	85-93	9
α-helix	97-102	6
α-helix	104-105	2
β-strand	108-109	2	3
α-helix	110-113	4
α-helix	115-118	4
β-strand	124-130	7	4
β-strand	136	1	5
β-strand	139	1	5
β-strand	141-147	7	4
β-strand	153-158	6	4
α-helix	163-173	11
β-strand	181-184	4	4
α-helix	188-191	4
α-helix	193-200	8
α-helix	204	1
β-strand	205-208	4	4
α-helix	209-210	2
α-helix	214-217	4
α-helix	218-234	17
α-helix	243-245	3
α-helix	246-254	9
α-helix	256-257	2
β-strand	258	1	6
β-strand	263	1	6
α-helix	265-270	6
α-helix	288-300	13
α-helix	308-311	4
β-strand	314-315	2	3
β-strand	322-325	4	7
β-strand	326	1	8
α-helix	327	1
α-helix	330-331	2
β-strand	337	1	8
α-helix	338-340	3
β-strand	341-342	2	7
β-strand	343-348	6	9
β-strand	351-355	5	9
β-strand	361-365	5	9
α-helix	366-368	3
β-strand	369-371	3	7
α-helix	372	1

Chain B: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	117-119	3
β-strand	124-130	7	10
β-strand	136	1	11
β-strand	139	1	11
β-strand	141-147	7	10
β-strand	153-158	6	10
α-helix	163-173	11
β-strand	181-184	4	10
α-helix	188-191	4
α-helix	193-201	9
α-helix	204	1
β-strand	205-208	4	10
α-helix	209-210	2
α-helix	218-235	18
α-helix	242-254	13
α-helix	265-270	6
α-helix	286-287	2
α-helix	288-297	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrase	A, B	protein	395	HUMAN SPUMARETROVIRUS	P14350
19 nucleotide preprocessed pfv donor DNA (non-transferred strand)	C	DNA	19	HUMAN SPUMARETROVIRUS
17 nucleotide preprocessed pfv donor DNA (transferred strand)	D	DNA	17	HUMAN SPUMARETROVIRUS

Sequence of entity 1 (A, B), FASTA

>4BDY_1 INTEGRASE (chains A, B)
GPGCNTKKPNLDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKI
VLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDR
PQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIA
IPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVG
RPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQE
IRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDH
LGNNRTVSIDNLKPTSHQNGTTNDTATMDHLEKNE

Sequence of entity 2 (C), FASTA

>4BDY_2 19 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND) (chains C)
ATTGTCATGGAATTTCGCA

Sequence of entity 3 (D), FASTA

>4BDY_3 17 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND) (chains D)
TGCGAAATTCCATGACA

Ligands and cofactors

ID	Name	Formula	Copies
CIJ	2-(3-chloro-4-fluorobenzyl)-4,5-dihydroxy-1H-isoindole-1,3(2H)-dione	C15 H9 Cl F N O4	1
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	1

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

Primary citation

Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase. Metifiot, M., Maddali, K., Johnson, B.C. et al. ACS Chem Biol (2013) 8:209. DOI 10.1021/CB300471N · 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.
3DLR 2.2 Å, Crystal structure of the catalytic core domain from PFV integrase
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…
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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