SMTL ID : 9bs4.2 (1 other biounit)

DNA Ligase 1 E346A/E592A double mutant with 5'-rG:C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x G- DT- DC- DG- DG- DA- DC: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')

G-DT-DC-DG-DG-DA-DC.1: 15 residues within 4Å: Chain A: A.44, R.45, R.329, R.478, K.484 Chain B: G.11 Chain C: G.1, T.2, C.3, C.4, G.5, A.6, C.7, C.8 Ligands: AMP.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.45, A:G.193, A:A.195, A:Q.197, A:S.198, A:Q.376, A:T.379 Water bridges: A:R.191, A:R.191, A:L.192, A:L.194, A:R.297 Salt bridges: A:R.297, A:K.477, A:H.480

1 x AMP: ADENOSINE MONOPHOSPHATE

AMP.2: 15 residues within 4Å: Chain A: L.284, E.306, Y.307, K.308, Y.309, R.313, E.361, F.400, E.460, M.463, K.465, W.482, K.484, K.486 Ligands: G-DT-DC-DG-DG-DA-DC.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.306, A:Y.309, A:R.313, A:R.329, A:K.465 Water bridges: A:R.478, A:K.484, A:K.486 Salt bridges: A:K.308, A:K.484, A:K.486 pi-Stacking: A:F.400

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balu, K.E. et al., Structures of LIG1 uncover the mechanism of sugar discrimination against 5'-RNA-DNA junctions during ribonucleotide excision repair. J.Biol.Chem. (2024)

Release Date

2024-09-25

Peptides

DNA ligase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

DNA ligase 1

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