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Tdg enzyme-substrate complex

Analyse Tdg enzyme-substrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HF7
Type: protein + DNA
Length: 253 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: G/T mismatch-specific thymine DNA glycosylase; DNA (28-mer)
EC: 3.2.2.29
UniProt: Q13569
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.29)	protein	197	42% helix, 13% strand	Q13569
C	DNA (28-mer)	dna	28	—	—
D	DNA (28-mer)	dna	28	—	—

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	602	0.67	0.77	32	empty
2	130	0.60	0.85	25	empty
3	97	0.40	0.77	24	empty
4	56	0.36	0.79	16	empty

Interfaces

3 interfaces between chains.

C–D · 1226 Å² buried · 119 hydrogen bonds · nucleic-nucleic
A–D · 911 Å² buried · 30 hydrogen bonds · protein-nucleic
A–C · 509 Å² buried · 6 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

5HF7 · TDG enzyme-substrate complex · the same entry in another collection · chain A against A, TM-score 1.00
Q13569 · AlphaFold monomer V2.0 prediction for G/T mismatch-specific thymine DNA glycosylase… · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q13569
Elsewhere: RCSB PDB 5HF7 · PDBe 5HF7 · UniProt Q13569

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