SMTL ID : 9ewg.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

DG-DC-DC-DG.1: 22 residues within 4Å: Chain A: Y.27, W.34, R.35, L.37, G.38, Y.39, A.42, 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.4, CA.12 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.34, A:W.34 Hydrogen bonds: A:R.269, A:R.272, A:R.293 Water bridges: A:K.41, A:K.276, A:K.276 Salt bridges: 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: 26 residues within 4Å: Chain A: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, Q.133, 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.3, NA.5, TMP.13 Protein-ligand interaction information (PLIP) not available

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

NA.3: 6 residues within 4Å: Chain A: D.187, D.189, R.243, D.245 Ligands: DC-DA-DG-DT-DA-DC.2, TMP.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.187, A:D.189 NA.4: 7 residues within 4Å: Chain A: C.60, S.61, I.62, P.63, G.64, I.65 Ligands: DG-DC-DC-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.65, A:I.65 NA.5: 8 residues within 4Å: Chain A: S.99, N.100, I.101, W.102, G.103, A.104, G.105 Ligands: DC-DA-DG-DT-DA-DC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.103, A:A.104, A:A.104

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

EDO.6: 4 residues within 4Å: Chain A: N.100, W.102, F.143, L.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.100, A:N.100 Water bridges: A:W.102 EDO.7: 7 residues within 4Å: Chain A: L.208, D.209, R.212, L.217, D.220, K.223, Y.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.208, A:D.209 EDO.8: 5 residues within 4Å: Chain A: Y.113, Q.114, Q.115, G.116, R.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.114, A:R.118 EDO.10: 2 residues within 4Å: Chain A: Q.164, A.165 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: G.176, S.177, D.187 Ligands: TMP.13 No protein-ligand interaction detected (PLIP) CA.12: 3 residues within 4Å: Chain A: R.68 Ligands: DG-DC-DC-DG.1, DG-DC-DC-DG.1 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 2 residues within 4Å: Chain A: R.124, S.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.124, A:R.124

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

TMP.13: 15 residues within 4Å: Chain A: G.176, R.180, D.187, D.189, 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, NA.3, CA.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.265 Hydrogen bonds: A:R.180, A:D.187, A:N.268 Water bridges: A:S.177, A:S.177, A:D.189, A:A.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nourisson, A. et al., DNA Polymerase Lambda I493K, 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