SMTL ID : 9ewe.1

DNA Polymerase Lambda I493K, E529D, Ca2+ Ground State Ternary Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.04 Å

Oligo State

monomer

Ligands

1 x DG- DC- DC- DG: DNA primer strand downstream(Non-covalent)

DG-DC-DC-DG.1: 19 residues within 4Å: Chain A: Y.27, W.34, R.35, G.38, Y.39, I.62, P.63, G.64, I.65, G.66, K.67, R.68, M.69, K.72 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.34 Hydrogen bonds: A:R.272 Salt bridges: A:K.41, A:R.269, A:K.276, A:K.276 pi-Stacking: A:W.34, A:W.34

1 x DC- DA- DG- DT- DA- DC: DNA primer strand upstream(Non-covalent)

DC-DA-DG-DT-DA-DC.2: 23 residues within 4Å: Chain A: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, D.189, K.227, L.229, R.243, D.245, Y.260, F.261 Chain B: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: NA.4 Protein-ligand interaction information (PLIP) not available

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: S.177, D.187 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.177, H2O.1

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: S.99, N.100, I.101, W.102, A.104 Ligands: DC-DA-DG-DT-DA-DC.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.104 NA.5: 2 residues within 4Å: Chain A: C.60 Ligands: DG-DC-DC-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nourisson, A. et al., Fidelity, specialization, and evolution of Paramecium PolX DNA polymerases involved in programmed double-strand break DNA repair. Nucleic Acids Res. (2025)

Release Date

2025-07-23

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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