2D07: SUMO-3-modified Thymine-DNA Glycosylase

Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase. Determined by X-ray diffraction at 2.1 Å resolution. Released 6 Jun 2006.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,381
Mol. weight: 36.8 kDa
Released: 6 Jun 2006

Explore 2D07 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2D07 contains 12 α-helices and 16 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: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	122-123	2	1
β-strand	127	1	2
β-strand	134-138	5	2
α-helix	143-148	6
β-strand	157	1	3
α-helix	159-165	7
α-helix	175-180	6
α-helix	181-185	5
β-strand	187-191	5	2
β-strand	195-196	2	1
α-helix	205-222	18
β-strand	226-230	5	2
α-helix	232-238	7
α-helix	239-243	5
β-strand	253-258	6	2
β-strand	265-269	5	2
β-strand	273	1	3
α-helix	282-284	3
α-helix	286-300	15
β-strand	308-314	7	4
α-helix	317-329	13

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	17-23	7	4
β-strand	29-35	7	4
α-helix	40-51	12
α-helix	55-57	3
β-strand	58-62	5	4
β-strand	65-66	2	4
β-strand	82-88	7	4

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 SMT3B	B	protein	93	Homo sapiens	P61956 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2D07_1 G/T mismatch-specific thymine DNA glycosylase (chains A)
GSNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLS
EVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVF
NGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYY
IKLKDLRDQLKGIERNMDVQEVQYTFDLQLAQEDAKKMAVKEEKYDPGYE

Sequence of entity 2 (B), FASTA

>2D07_2 Ubiquitin-like protein SMT3B (chains B)
MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRF
RFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG

Primary citation

Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase. Baba, D., Maita, N., Jee, J.G. et al. J Mol Biol (2006) 359:137-147. DOI 10.1016/j.jmb.2006.03.036 · 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
1WYW 2.1 Å, Crystal Structure of SUMO1-conjugated thymine DNA glycosylase
5T2W 2.2 Å, Structure of thymine DNA glycosylase bound to substrate analog 2'-F-5-formyl-dC

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