SMTL ID : 7sum.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG- DA- DC: DNA(5'-P*GP*TP*CP*GP*GP*AP*C-3')(Non-covalent)

DG-DT-DC-DG-DG-DA-DC.1: 23 residues within 4Å: Chain A: S.43, R.329, K.484, K.486, Y.489, K.510, T.538, G.539, F.540, S.541, D.542, F.612, R.614 Chain B: A.11 Chain C: G.1, T.2, C.3, C.4, G.5, A.6, C.7, T.8 Ligands: AMP.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: 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:R.383, A:R.508, A:K.510, A:K.510, A:K.510, A:K.535, A:S.590, A:Y.595, A:S.609 Water bridges: A:L.194, A:K.535, A:K.535, A:K.535 Salt bridges: A:R.191, A:K.244, A:R.478, A:K.535, A:K.535

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 13 residues within 4Å: Chain A: E.306, Y.307, K.308, Y.309, R.313, E.361, F.400, M.463, K.465, W.482, K.484 Ligands: DG-DT-DC-DG-DG-DA-DC.1, DG-DT-DC-DG-DG-DA-DC.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.306, A:E.306, A:K.308, A:Y.309, A:R.313, A:K.465 Salt bridges: A:K.308, A:K.484 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