SMTL ID : 7kr4.1

Human DNA Ligase 1(E346A/E592A) Bound to a nicked DNA substrate control duplex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

DA-DT-DT-DC-DT-DG-DC.1: 27 residues within 4Å: Chain A: S.46, A.47, R.48, R.292, K.311, R.332, K.487, K.489, Y.492, T.541, G.542, F.543, S.544, D.545, F.615, R.617 Chain B: C.11 Chain C: G.1, C.2, A.3, G.4, A.5, A.6, T.7, G.8 Ligands: ACT.3, AMP.6 32 PLIP interactions: 32 interactions with chain A Hydrogen bonds: A:R.48, A:R.48, A:R.194, A:L.195, A:G.196, A:L.197, A:A.198, A:A.198, A:Q.200, A:S.201, A:R.300, A:Q.379, A:T.382, A:R.386, A:R.386, A:R.511, A:K.513, A:K.513, A:K.538, A:S.593, A:S.612 Water bridges: A:K.247, A:R.511, A:R.514, A:R.514, A:T.541, A:F.615 Salt bridges: A:R.194, A:K.247, A:H.289, A:K.538, A:K.538

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: Y.526, E.531, Y.566, E.628 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.628 ACT.3: 5 residues within 4Å: Chain A: V.45, S.46, A.47, R.50 Ligands: DA-DT-DT-DC-DT-DG-DC.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.45, A:A.47, A:R.50 Hydrogen bonds: A:S.46, A:A.47 ACT.4: 6 residues within 4Å: Chain A: P.215, G.216, L.264, E.265, H.266, R.270 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.270 ACT.5: 5 residues within 4Å: Chain A: V.210, H.266, G.267, L.268, E.269 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.269 Hydrogen bonds: A:L.268

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.6: 13 residues within 4Å: Chain A: E.309, Y.310, K.311, Y.312, R.316, R.332, E.364, F.403, M.466, K.468, W.485, K.487 Ligands: DA-DT-DT-DC-DT-DG-DC.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.309, A:Y.312, A:R.316, A:R.332, A:K.468 Water bridges: A:K.311, A:Y.492 Salt bridges: A:K.311, A:K.487 pi-Stacking: A:F.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, J.S. et al., High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication. Nat Commun (2021)

Release Date

2021-02-03

Peptides

DNA ligase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase 1

Related Entries With Identical Sequence