SMTL ID : 4xeg.1

Structure of the enzyme-product complex resulting from TDG action on a G/hmU mismatch

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: N.27, L.28, Q.119, P.120, R.121 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.119, A:R.121 Water bridges: A:N.27, A:N.27, A:N.27, A:L.28 EDO.2: 2 residues within 4Å: Chain A: H.183, I.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.183 Water bridges: A:H.183

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 6 residues within 4Å: Chain A: G.34, I.35, N.36, Y.48, N.87 Chain C: X.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.48 Hydrogen bonds: A:I.35 Water bridges: A:G.38, A:N.53 ACY.4: 3 residues within 4Å: Chain A: E.66, K.80, Y.81 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.81 ACY.5: 3 residues within 4Å: Chain A: V.143, N.145, P.152 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.143, A:P.152 Hydrogen bonds: A:N.145 Water bridges: A:E.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malik, S.S. et al., Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA. Nucleic Acids Res. (2015)

Release Date

2015-09-09

Peptides

G/T mismatch-specific thymine DNA glycosylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G/T mismatch-specific thymine DNA glycosylase

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