1WYW: SUMO1-conjugated thymine DNA glycosylase

Crystal Structure of SUMO1-conjugated thymine DNA glycosylase. Determined by X-ray diffraction at 2.1 Å resolution. Released 21 Jun 2005.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,538
Mol. weight: 37.58 kDa
Ligands: MG
Released: 21 Jun 2005

Explore 1WYW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1WYW contains 18 α-helices and 14 β-strands across 2 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	119-121	3
β-strand	127	1	1
β-strand	134-138	5	1
α-helix	143-148	6
β-strand	157	1	2
α-helix	159-165	7
α-helix	175-180	6
α-helix	181-185	5
β-strand	187-191	5	1
α-helix	200-202	3
α-helix	205-222	18
β-strand	226-230	5	1
α-helix	232-238	7
α-helix	239-243	5
β-strand	253-254	2	1
α-helix	257-258	2
β-strand	265-269	5	1
β-strand	273	1	2
α-helix	282-284	3
α-helix	286-299	14
α-helix	302-304	3
β-strand	308-314	7	3
α-helix	317-329	13

Chain B: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	21-27	7	3
β-strand	33-39	7	3
α-helix	45-55	11
α-helix	59-61	3
β-strand	62-66	5	3
β-strand	69-70	2	3
α-helix	71-72	2
α-helix	77-80	4
β-strand	87-92	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G/T mismatch-specific thymine DNA glycosylase	A	protein	230	Homo sapiens	Q13569 (AlphaFold model)
Ubiquitin-like protein SMT3C	B	protein	97	Homo sapiens	P63165 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1WYW_1 G/T mismatch-specific thymine DNA glycosylase (chains A)
GSNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLS
EVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVF
NGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYY
IKLKDLRDQLKGIERNMDVQEVQYTFDLQLAQEDAKKMAVKEEKYDPGYE

Sequence of entity 2 (B), FASTA

>1WYW_2 Ubiquitin-like protein SMT3C (chains B)
MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMN
SLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	5

Water and common crystallization additives (NA, CL) are not listed.

Primary citation

Crystal structure of thymine DNA glycosylase conjugated to SUMO-1. Baba, D., Maita, N., Jee, J.G. et al. Nature (2005) 435:979-982. DOI 10.1038/nature03634 · PubMed

Other PDB entries of the same protein (UniProt Q13569 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4Z47 1.45 Å, Structure of the enzyme-product complex resulting from TDG action on a GU mismatch in…
5HF7 1.54 Å, TDG enzyme-substrate complex
6U17 1.55 Å, Human thymine DNA glycosylase bound to DNA with 2'-F-5-carboxyl-dC substrate analog
6U16 1.6 Å, Human thymine DNA glycosylase N140A mutant bound to DNA with 5-carboxyl-dC substrate
5FF8 1.7 Å, TDG enzyme-product complex
5JXY 1.71 Å, Enzyme-substrate complex of TDG catalytic domain bound to a G/U analog
4XEG 1.72 Å, Structure of the enzyme-product complex resulting from TDG action on a G/hmU mismatch
4Z3A 1.72 Å, Acetate-free structure of the enzyme-product complex resulting from TDG action on a GU…
4Z7Z 1.83 Å, Structure of the enzyme-product complex resulting from TDG action on a GT mismatch in…
4Z7B 2.02 Å, Structure of the enzyme-product complex resulting from TDG action on a GfC mismatch
2D07 2.1 Å, Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase
5T2W 2.2 Å, Structure of thymine DNA glycosylase bound to substrate analog 2'-F-5-formyl-dC

Browse structure collections

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