SMTL ID : 7sxe.1

Crystal structure of ligase I with nick duplexes containing cognate G:T

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG- DA- DC: DNA chain 2(Non-covalent)

DG-DT-DC-DG-DG-DA-DC.1: 22 residues within 4Å: Chain A: S.43, A.44, R.329, Y.489, K.510, T.538, G.539, F.540, S.541, D.542, F.612, R.614 Chain B: G.11 Chain C: G.1, T.2, C.3, C.4, G.5, A.6, C.7, T.8 Ligands: AMP.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:R.511 Hydrogen bonds: A:R.45, A:R.45, A:R.189, A:L.192, A:G.193, A:L.194, A:A.195, A:Q.197, A:S.198, A:S.198, A:Q.376, A:T.379, A:T.379, A:R.383, A:R.508, A:K.510, A:K.510, A:K.510, A:K.535, A:S.590, A:Y.595 Water bridges: A:K.510 Salt bridges: A:R.191, A:K.535, A:K.535

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 12 residues within 4Å: Chain A: E.306, Y.307, K.308, Y.309, R.313, E.361, F.400, A.436, M.463, K.465, W.482 Ligands: DG-DT-DC-DG-DG-DA-DC.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.306, A:E.306, A:Y.309, A:R.313, A:K.465 Salt bridges: A:K.308 pi-Stacking: A:F.400

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, Q. et al., Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair. Nat Commun (2022)

Release Date

2022-07-13

Peptides

DNA ligase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase 1

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