SMTL ID : 9ewd.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

monomer

Ligands

1 x DG- DC- DC- DG: DNA primer strand downstream (5'P)(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: K.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.34, A:W.34 Hydrogen bonds: A:W.34, A:R.272, A:R.293 Salt bridges: A:K.41, A:R.269, A:K.276, A:K.276 pi-Stacking: A:W.34

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

DC-DA-DG-DT-DA-DC.2: 22 residues within 4Å: Chain A: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, 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: TMP.3, NA.4 Protein-ligand interaction information (PLIP) not available

1 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.3: 15 residues within 4Å: Chain A: G.176, D.187, D.189, D.245, Y.260, F.261, T.262, G.263, S.264, A.265, N.268 Chain B: A.5 Ligands: DC-DA-DG-DT-DA-DC.2, CA.11, NA.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.265 Hydrogen bonds: A:D.187, A:Y.260, A:F.261, A:N.268 Water bridges: A:R.180

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

NA.4: 4 residues within 4Å: Chain A: S.99, I.101, A.104 Ligands: DC-DA-DG-DT-DA-DC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.101, A:G.103, A:A.104 NA.12: 7 residues within 4Å: Chain A: D.187, V.188, D.189, R.243, L.244, D.245 Ligands: TMP.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.187, A:V.188

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: N.100, I.101, W.102, F.143, L.144 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.102 EDO.6: 3 residues within 4Å: Chain A: R.212, L.217, D.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.212 Water bridges: A:D.220 EDO.7: 4 residues within 4Å: Chain A: Y.113, Q.114, G.116, R.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.114, A:G.116, A:R.118, A:R.118

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: R.233, H.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.233 Water bridges: A:D.142

2 x K: POTASSIUM ION(Non-covalent)

K.9: 6 residues within 4Å: Chain A: C.60, I.62, P.63, G.64, I.65 Ligands: DG-DC-DC-DG.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.60, A:I.62, H2O.3, H2O.6 K.10: 3 residues within 4Å: Chain A: I.123, R.124, A.127 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.124, A:A.127, H2O.6

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 3 residues within 4Å: Chain A: S.177, D.187 Ligands: TMP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nourisson, A. et al., DNA Polymerase Lambda I493K E529D, TTP:At Ca2+ Ground State Ternary Complex. To be published

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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