SMTL ID : 9lnp.1

the hUNG bound to DNA product embedding uridine ribonucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

1 x DT- DG- DT- RP5- DA- DT- DC- DT- DT: DNA (5'-D(*TP*GP*T*(RP5)P*AP*TP*CP*TP*T)-3')(Non-covalent)

DT-DG-DT-RP5-DA-DT-DC-DT-DT.1: 30 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: Q.64, D.65, Y.67, H.68, Q.72, F.78, P.87, P.88, S.89, A.134, N.135, G.166, S.167, Y.168, A.187, H.188, S.190, P.191, L.192, S.193, R.196 12 PLIP interactions: 12 interactions with chain B Water bridges: B:R.196, B:D.65, B:D.65, B:Y.67, B:H.68, B:H.68, B:Q.72, B:Q.72 Hydrogen bonds: B:Q.64, B:D.65, B:S.89, B:S.89 Salt bridges: B:H.188

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain B: P.66, Y.67, A.73, L.76, C.77, F.78, N.124 No protein-ligand interaction detected (PLIP)

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