5OYM: PC4 and SFRS1-interacting protein

HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor. Determined by X-ray diffraction at 2.05 Å resolution. Released 7 Mar 2018.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 8
Atoms: 6,129
Mol. weight: 95.18 kDa
Released: 7 Mar 2018

Explore 5OYM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OYM contains 46 α-helices and 10 β-strands across 8 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: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	347-362	16
β-strand	363-364	2	2
β-strand	367-368	2	2
α-helix	370-382	13
α-helix	387-391	5
α-helix	394-405	12
α-helix	410-425	16

Chain B: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	347-362	16
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	410-424	15

Chain C: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	347-362	16
α-helix	370-382	13
α-helix	387-390	4
α-helix	391-393	3
α-helix	394-405	12
α-helix	410-425	16

Chain D: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	347-362	16
α-helix	370-382	13
α-helix	387-390	4
α-helix	391-393	3
α-helix	394-403	10
α-helix	410-424	15
α-helix	426-428	3

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	347-362	16
β-strand	363-364	2	4
β-strand	367-368	2	4
α-helix	370-382	13
α-helix	387-391	5
α-helix	394-403	10
α-helix	410-426	17

Chain F: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	347-362	16
β-strand	363-364	2	5
β-strand	367-368	2	5
α-helix	370-382	13
α-helix	387-390	4
α-helix	391-393	3
α-helix	394-405	12
α-helix	410-429	20

Chain G: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	347-362	16
α-helix	365-367	3
α-helix	370-382	13
α-helix	387-391	5
α-helix	394-403	10
α-helix	410-429	20

Chain H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	347-362	16
β-strand	363-364	2	1
β-strand	367-368	2	1
α-helix	370-382	13
α-helix	387-391	5
α-helix	394-403	10
α-helix	410-425	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PC4 and SFRS1-interacting protein	A, B, C, D, E, F, G, H	protein	111	Homo sapiens	O75475 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>5OYM_1 PC4 and SFRS1-interacting protein (chains A, B, C, D, E, F, G, H)
GGSMGSGGGGSGGGGSGGGGAAAMETSMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDEL
ASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFLVGE

Primary citation

Cloning, purification and structure determination of the HIV integrase-binding domain of lens epithelium-derived growth factor. Hannon, C., Cruz-Migoni, A., Platonova, O. et al. Acta Crystallogr F Struct Biol Commun (2018) 74:143-149. DOI 10.1107/S2053230X18001553 · PubMed

Other PDB entries of the same protein (UniProt O75475 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TRJ 1.3 Å, LEDGF/p75 IBD dimer
9S81 1.63 Å, Crystal structure of the LEDGF PWWP domain
5N88 1.7 Å, Crystal structure of antibody bound to viral protein
2B4J 2.02 Å, Structural basis for the recognition between HIV-1 integrase and LEDGF/p75
4FU6 2.1 Å, Crystal structure of the PSIP1 PWWP domain
9S83 2.1 Å, Crystal structure of de novo designed binder JUBO4 and the LEDGF PWWP domain
3HPH 2.64 Å, Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD
8PEO 2.69 Å, H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex
9S28 2.8 Å, MVV STC intasome in complex with LEDGF
9S29 2.8 Å, MVV CSC intasome in complex with LEDGF
3U88 3.0 Å, Crystal structure of human menin in complex with MLL1 and LEDGF
7OUF 3.0 Å, Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor XZ450

Browse structure collections

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