MolNFT v1 · #134396 · protein + DNA

Structure of thymine DNA glycosylase bound to substrate analog 2'-F-5- formyl-dc

5T2W · G/T mismatch-specific thymine DNA glycosylase: “Structure of thymine DNA glycosylase bound to substrate analog 2'-F-5- formyl-dc”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #134396 on GenesisL1: 3D structure…

PDB: 5T2W
Type: protein + DNA
Length: 250 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); DNA (27-mer)
EC: 3.2.2.29
UniProt: Q13569
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 41% 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	195	41% helix, 13% strand	Q13569
C	DNA (28-mer)	dna	28	—	—
D	DNA (27-mer)	dna	27	—	—

Pockets

3 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	507	0.69	0.79	28	empty
2	108	0.63	0.89	20	empty
3	129	0.46	0.78	23	empty

Interfaces

3 interfaces between chains.

C–D · 1187 Å² buried · 127 hydrogen bonds · nucleic-nucleic
A–D · 942 Å² buried · 32 hydrogen bonds · protein-nucleic
A–C · 629 Å² buried · 10 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

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 5T2W · PDBe 5T2W · UniProt Q13569

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