5AYR: SAUGI/human UDG complex

The crystal structure of SAUGI/human UDG complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 8 Jun 2016.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Staphylococcus aureus
Chains: 4
Atoms: 6,002
Mol. weight: 80.06 kDa
Ligands: MG
Released: 8 Jun 2016

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

Secondary structure: helices and β-sheets

5AYR contains 42 α-helices and 25 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.

Chain A: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	87-93	7
α-helix	94-96	3
α-helix	100-115	16
β-strand	118-119	2	1
α-helix	122-124	3
α-helix	127-129	3
α-helix	134-136	3
β-strand	139-143	5	2
α-helix	165-167	3
α-helix	168-180	13
α-helix	193-197	5
β-strand	200-204	5	2
β-strand	209-210	2	1
β-strand	213	1	1
α-helix	222-235	14
β-strand	241-245	5	2
α-helix	246-252	7
β-strand	262-266	5	2
α-helix	274-276	3
α-helix	283-293	11
α-helix	297-299	3

Chain B: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	21-23	3
β-strand	24-31	8	3
α-helix	32-34	3
α-helix	38-40	3
α-helix	49	1
β-strand	50-57	8	3
α-helix	59-64	6
β-strand	67-73	7	3
β-strand	76-83	8	3
β-strand	89-95	7	3
β-strand	100-103	4	3
α-helix	105-108	4

Chain C: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	87-93	7
α-helix	94-96	3
α-helix	100-115	16
β-strand	118-119	2	4
α-helix	122-124	3
α-helix	127-129	3
α-helix	134-136	3
β-strand	139-143	5	5
α-helix	165-167	3
α-helix	168-180	13
α-helix	184-186	3
α-helix	193-197	5
β-strand	200-204	5	5
β-strand	209-210	2	4
α-helix	222-235	14
β-strand	241-245	5	5
α-helix	247-252	6
β-strand	262-266	5	5
α-helix	274-276	3
α-helix	283-293	11
α-helix	297-299	3

Chain D: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	21-23	3
β-strand	24-31	8	6
α-helix	32-34	3
α-helix	38-40	3
β-strand	50-57	8	6
α-helix	59-64	6
β-strand	67-73	7	6
β-strand	76-83	8	6
β-strand	89-95	7	6
β-strand	100-103	4	6
α-helix	105-108	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uracil-DNA glycosylase	A, C	protein	231	Homo sapiens	P13051 (AlphaFold model)
Uncharacterized protein	B, D	protein	112	Staphylococcus aureus	Q936H5 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5AYR_1 Uracil-DNA glycosylase (chains A, C)
MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVI
LGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVL
LLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRH
HVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKELLEHHHHHH

Sequence of entity 2 (B, D), FASTA

>5AYR_2 Uncharacterized protein (chains B, D)
MTLELQLKHYITNLFNLPKDEKWECESIEEIADDILPDQYVRLGALSNKILQTYTYYSDT
LHESNIYPFILYYQKQLIAIGYIDENHDMDFLYLHNTIMPLLDQRYLLTGGQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4

Primary citation

Using structural-based protein engineering to modulate the differential inhibition effects of SAUGI on human and HSV uracil DNA glycosylase. Wang, H.C., Ho, C.H., Chou, C.C. et al. Nucleic Acids Res (2016) 44:4440-4449. DOI 10.1093/nar/gkw185 · PubMed

Other PDB entries of the same protein (UniProt P13051 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FCI 1.27 Å, Complex of UNG2 and a fragment-based designed inhibitor
2HXM 1.3 Å, Complex of UNG2 and a small Molecule synthetic Inhibitor
3TKB 1.5 Å, crystal structure of human uracil-DNA glycosylase D183G/K302R mutant
1AKZ 1.57 Å, Human uracil-DNA glycosylase
3FCK 1.64 Å, Complex of UNG2 and a fragment-based design inhibitor
3FCL 1.7 Å, Complex of UNG2 and a fragment-based designed inhibitor
9LNQ 1.74 Å, The hUNG bound to DNA product embedding 4primer-OCH3-dU
9LNP 1.76 Å, the hUNG bound to DNA product embedding uridine ribonucleotide
1EMH 1.8 Å, Crystal structure of human uracil-DNA glycosylase bound to uncleaved…
6VBA 1.8 Å, Structure of human Uracil DNA Glycosylase (UDG) bound to Aurintricarboxylic acid (ATA)
3FCF 1.84 Å, Complex of UNG2 and a fragment-based designed inhibitor
1Q3F 1.9 Å, Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA

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