SMTL ID : 7kr3.1

Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 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: 25 residues within 4Å: Chain A: S.46, A.47, R.48, 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.12 Chain C: G.1, C.2, A.3, G.4, A.5, A.6, T.7, G.8 Ligands: AMP.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:R.48, A:R.48, A:R.192, A:G.196, A:L.197, A:A.198, A:Q.200, A:Q.200, A:S.201, A:Q.379, A:R.511, A:K.513, A:K.513, A:K.513, A:K.538, A:S.593, A:Y.598, A:S.612, A:S.612 Salt bridges: A:K.247, A:H.289, A:K.538, A:K.538

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 16 residues within 4Å: Chain A: A.288, E.309, Y.310, K.311, Y.312, R.316, R.332, E.364, F.403, A.439, M.466, K.468, W.485, K.487 Ligands: DA-DT-DT-DC-DT-DG-DC.1, DA-DT-DT-DC-DT-DG-DC.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.309, A:E.309, A:Y.312, A:R.316, A:R.332, A:K.468 Salt bridges: A:K.311, A:K.487 pi-Stacking: A:F.403

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

ACT.3: 2 residues within 4Å: Chain C: G.9, G.10 No protein-ligand interaction detected (PLIP)

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

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