SMTL ID : 9lnq.1

The hUNG bound to DNA product embedding 4primer-OCH3-dU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x DT- DG- DT- KBC- DA- DT- DC- DT- DT: DNA (5'-D(*TP*GP*TP*(KBC)P*AP*TP*CP*TP*T)-3')(Non-covalent)

DT-DG-DT-KBC-DA-DT-DC-DT-DT.1: 34 residues within 4Å: Chain A: A.2, A.3, G.4, A.5, T.6, A.7, A.8, C.9, A.10 Chain B: G.62, Q.63, D.64, P.65, Y.66, H.67, Q.71, C.76, F.77, P.86, P.87, S.88, N.123, A.133, G.165, S.166, Y.167, A.186, H.187, S.189, P.190, L.191, S.192, R.195 Ligands: NA.2 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:P.190, B:Y.194, B:Q.63, B:Q.63, B:D.64, B:F.77, B:S.88, B:S.88, B:N.123, B:N.123 Water bridges: B:H.67, B:Q.71 pi-Stacking: B:Y.66, B:F.77

3 x NA: SODIUM ION(Non-functional Binders)

NA.2: 8 residues within 4Å: Chain B: P.65, Y.66, A.72, L.75, C.76, F.77, N.123 Ligands: DT-DG-DT-KBC-DA-DT-DC-DT-DT.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.66, B:L.75, B:F.77, B:N.123 Water bridges: B:H.73, B:G.74 NA.3: 4 residues within 4Å: Chain B: R.32, Y.35, T.36, V.37 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.32, B:V.37, B:V.37 NA.4: 3 residues within 4Å: Chain B: K.18, P.19, Y.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.20 Water bridges: B:Q.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., Uridine Embedded within DNA is Repaired by Uracil DNA Glycosylase via a Mechanism Distinct from That of Ribonuclease H2. J.Am.Chem.Soc. (2025)

Release Date

2025-04-16

Peptides

Uracil-DNA glycosylase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
E

Uracil-DNA glycosylase