3F9K: Two domain fragment of HIV-2 integrase

Two domain fragment of HIV-2 integrase in complex with LEDGF IBD. Determined by X-ray diffraction at 3.2 Å resolution. Released 20 Jan 2009.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Human immunodeficiency virus type 2, Homo sapiens
Chains: 36
Atoms: 46,740
Mol. weight: 703.19 kDa
Ligands: ZN, MG
Released: 20 Jan 2009

Explore 3F9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3F9K contains 313 α-helices and 192 β-strands across 36 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: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	348-361	14
β-strand	363-364	2	51
β-strand	367-368	2	51
α-helix	370-381	12
α-helix	387-390	4
α-helix	394-403	10
α-helix	410-429	20
α-helix	435-439	5

Chains A, c, E, g, I, k, M, o, Q, s, U and Y: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-26	8
α-helix	30-38	9
β-strand	60-68	9	1
β-strand	71-78	8	1
β-strand	83-89	7	1
α-helix	94-105	12
β-strand	112-115	4	1
α-helix	124-133	10
β-strand	136-139	4	1
α-helix	142-144	3
α-helix	150-164	15
α-helix	166-168	3
α-helix	172-185	14
β-strand	189	1	2
β-strand	194	1	2
α-helix	196-205	10

Chains B, d, F, h, J, l, N, p, R, t, V and Z: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	5-15	11
α-helix	19-26	8
α-helix	30-38	9
β-strand	60-68	9	4
β-strand	71-78	8	4
β-strand	83-89	7	4
α-helix	94-105	12
β-strand	112-115	4	4
α-helix	124-133	10
β-strand	136-139	4	4
α-helix	150-165	16
α-helix	166-168	3
α-helix	172-185	14
β-strand	189	1	5
β-strand	194	1	5
α-helix	196-205	10

Chains C and K: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	348-361	14
β-strand	363-364	2	8
β-strand	367-368	2	8
α-helix	370-381	12
α-helix	387-392	6
α-helix	394-403	10
α-helix	410-429	20
α-helix	435-439	5

Chains e and S: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	348-361	14
β-strand	363-364	2	56
β-strand	367-368	2	56
α-helix	370-381	12
α-helix	387-392	6
α-helix	394-403	10
α-helix	410-427	18
α-helix	435-439	5

Chains G and W: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	348-361	14
β-strand	363-364	2	18
β-strand	367-368	2	18
α-helix	370-381	12
α-helix	387-390	4
α-helix	394-403	10
α-helix	410-427	18
α-helix	435-439	5

Chain i: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	348-361	14
β-strand	363-364	2	3
β-strand	367-368	2	3
α-helix	370-381	12
α-helix	387-390	4
α-helix	391-393	3
α-helix	394-403	10
α-helix	410-428	19
α-helix	435-439	5

Chain m: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	348-361	14
β-strand	363-364	2	13
β-strand	367-368	2	13
α-helix	370-381	12
α-helix	387-391	5
α-helix	394-403	10
α-helix	410-429	20
α-helix	435-439	5

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrase	A, B, E, F, I, J, M, N, Q, R, U, V, Y, Z, c, d, g, h, k, l, o, p, s, t	protein	210	Human immunodeficiency virus type 2	P04584
PC4 and SFRS1-interacting protein	C, G, K, O, S, W, a, e, i, m, q, u	protein	95	Homo sapiens	O75475 (AlphaFold model)

Sequence of entity 1 (A, B, E, F, I, J, M, N, Q, R, U, V, Y, Z, c, d, g, h, k, l, o, p, s, t), FASTA

>3F9K_1 Integrase (chains A, B, E, F, I, J, M, N, Q, R, U, V, Y, Z, c, d, g, h, k, l, o, p, s, t)
MVLEKIEPAQEEHEKYHSNVKELSHKFGIPNLVARQIVNSCAQCQQKGEAIHGQVNAELG
TWQMDCTHLEGKIIIVAVHVASGFIEAEVIPQESGRQTALFLLKLASRWPITHLHTDNGA
NFTSQEVKMVAWWIGIEQSFGVPYNPQSQGVVEAMNHHLKNQISRIREQANTIETIVLMA
VHCMNFKRRGGIGDMTPSERLINMITTEQE

Sequence of entity 2 (C, G, K, O, S, W, a, e, i, m, q, u), FASTA

>3F9K_2 PC4 and SFRS1-interacting protein (chains C, G, K, O, S, W, a, e, i, m, q, u)
SMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRF
KVSQVIMEKSTMLYNKFKNMFLVGEGDSVLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	24
MG	Magnesium ion	Mg	24

Primary citation

A novel co-crystal structure affords the design of gain-of-function lentiviral integrase mutants in the presence of modified PSIP1/LEDGF/p75. Hare, S., Shun, M.C., Gupta, S.S. et al. PLoS Pathog (2009) 5:e1000259-e1000259. DOI 10.1371/journal.ppat.1000259 · PubMed

Other PDB entries of the same protein (UniProt P04584), best resolution first:

3EC0 1.18 Å, High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-06579A
3ECG 1.18 Å, High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-98065
3EBZ 1.2 Å, High Resolution HIV-2 Protease Structure in Complex with Clinical Drug Darunavir
1IDA 1.7 Å, Crystal structures of HIV-2 protease in complex with inhibitors containing the…
1HSH 1.9 Å, Crystal structure at 1.9 Å resolution of human immunodeficiency virus (HIV) II protease…
4UPJ 1.9 Å, Human immunodeficiency virus type 2 protease mutant with lys 57 replaced by leu (K57L)…
2HPE 2.0 Å, Comparison of the structures of HIV-2 protease complexes in three crystal space groups…
1IDB 2.2 Å, Crystal structures of HIV-2 protease in complex with inhibitors containing the…
2MIP 2.2 Å, Crystal structure of human immunodeficiency virus (HIV) type 2 protease in complex with…
1HII 2.3 Å, Comparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex…
5UPJ 2.3 Å, HIV-2 PROTEASE/U99283 complex
6UPJ 2.34 Å, HIV-2 PROTEASE/U99294 complex

Browse structure collections

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