6VBA: Human Uracil DNA Glycosylase

Structure of human Uracil DNA Glycosylase (UDG) bound to Aurintricarboxylic acid (ATA). Determined by X-ray diffraction at 1.8 Å resolution. Released 3 Mar 2021.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,129
Mol. weight: 25.97 kDa
Ligands: QU4
Released: 3 Mar 2021

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

Secondary structure: helices and β-sheets

6VBA contains 15 α-helices and 6 β-strands across 1 chain. 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: 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	1
α-helix	122-124	3
α-helix	127-129	3
α-helix	134-136	3
β-strand	139-143	5	2
α-helix	146-147	2
α-helix	165-167	3
α-helix	168-180	13
α-helix	193-196	4
β-strand	200-204	5	2
β-strand	209-210	2	1
α-helix	222-236	15
β-strand	241-245	5	2
α-helix	247-252	6
β-strand	262-266	5	2
α-helix	274-276	3
α-helix	283-293	11
α-helix	297-299	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uracil-DNA glycosylase	A	protein	223	Homo sapiens	P13051 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VBA_1 Uracil-DNA glycosylase (chains A)
MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVI
LGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVL
LLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRH
HVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL

Ligands and cofactors

ID	Name	Formula	Copies
QU4	3,3'-[(3-carboxy-4-oxocyclohexa-2,5-dien-1-ylidene)methylene]bis(6-hydroxybenzo…	C22 H14 O9	1

Primary citation

An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation. Nguyen, M.T., Moiani, D., Ahmed, Z. et al. Prog Biophys Mol Biol (2021) 163:143-159. DOI 10.1016/j.pbiomolbio.2021.02.004 · 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…
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
1SSP 1.9 Å, Wild-type uracil-DNA glycosylase bound to uracil-containing DNA

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