6LYJ: SAUGI/EBVUDG complex

The crystal structure of SAUGI/EBVUDG complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 24 Jun 2020.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Epstein-Barr virus (strain GD1), Staphylococcus aureus
Chains: 4
Atoms: 6,232
Mol. weight: 84.02 kDa
Released: 24 Jun 2020

Explore 6LYJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LYJ contains 44 α-helices and 31 β-strands across 4 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.

Chains A and B: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	32-38	7
α-helix	42-59	18
β-strand	64-65	2	1
α-helix	68-70	3
α-helix	73-75	3
α-helix	80-82	3
β-strand	85-89	5	2
β-strand	98	1	3
β-strand	105	1	3
α-helix	110-112	3
α-helix	113-125	13
α-helix	138-142	5
β-strand	145-149	5	2
β-strand	154-155	2	1
β-strand	158	1	1
α-helix	167-181	15
β-strand	186-190	5	2
α-helix	191-195	5
α-helix	196-200	5
β-strand	207-211	5	2
α-helix	216-218	3
α-helix	228-229	2
α-helix	235-245	11
α-helix	248-251	4

Chain C: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
α-helix	22-23	2
β-strand	24-26	3	7
β-strand	29-31	3	7
α-helix	32-35	4
α-helix	38-40	3
α-helix	49	1
β-strand	50-57	8	7
α-helix	59-64	6
β-strand	67-73	7	7
β-strand	76-83	8	7
β-strand	89-95	7	7
β-strand	100-103	4	7
α-helix	105-107	3

Chain D: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	22-23	2
β-strand	24-31	8	8
α-helix	32-34	3
α-helix	38-40	3
α-helix	49	1
β-strand	50-57	8	8
α-helix	59-64	6
β-strand	67-73	7	8
β-strand	76-83	8	8
β-strand	89-95	7	8
β-strand	100-103	4	8
α-helix	105-107	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uracil-DNA glycosylase	A, B	protein	255	Epstein-Barr virus (strain GD1)	P12888 (AlphaFold model)
Saugi	C, D	protein	112	Staphylococcus aureus	Q936H5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6LYJ_1 Uracil-DNA glycosylase (chains A, B)
MASRGLDLWLDEHVWKRKQEIGVKGENLLLPDLWLDFLQLSPIFQRKLAAVIACVRRLRT
QATVYPEEDMCMAWARFCDPSDIKVVILGQDPYHGGQANGLAFSVAYGFPVPPSLRNIYA
ELHRSLPEFSPPDHGCLDAWASQGVLLLNTILTVQKGKPGSHADIGWAWFTDHVISLLSE
RLKACVFMLWGAKAGDKASLINSKKHLVLTSQHPSPLAQNSTRKSAQQKFLGNNHFVLAN
NFLREKGLGEIDWRL

Sequence of entity 2 (C, D), FASTA

>6LYJ_2 SAUGI (chains C, D)
MTLELQLKHYITNLFNLPKDEKWECESIEEIADDILPDQYVRLGALSNKILQTYTYYSDT
LHESNIYPFILYYQKQLIAIGYIDENHDMDFLYLHNTIMPLLDQRYLLTGGQ

Primary citation

Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases. Liao, Y.T., Lin, S.J., Ko, T.P. et al. Int J Biol Macromol (2020) 160:903-914. DOI 10.1016/j.ijbiomac.2020.05.267 · PubMed

Other PDB entries of the same protein (UniProt P12888 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2J8X 2.3 Å, Epstein-Barr virus uracil-DNA glycosylase in complex with Ugi from PBS-2

Browse structure collections

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