SMTL ID : 9ewb.1

DNA Polymerase Lambda I493R, TTP:At Ca2+ Ground State Ternary Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC.1: 27 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, R.247, Y.260, F.261 Chain B: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: NA.4, TTP.6, EDO.13 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: DNA (5'-D(P*GP*CP*CP*G)-3')(Non-covalent)

DG-DC-DC-DG.2: 21 residues within 4Å: Chain A: Y.27, W.34, R.35, L.37, G.38, Y.39, K.41, A.42, 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 Protein-ligand interaction information (PLIP) not available

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: G.176, S.177, D.187, D.189 Ligands: TTP.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.187, A:D.189, H2O.2

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

NA.4: 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.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.101, A:G.103, A:A.104 NA.5: 7 residues within 4Å: Chain A: C.60, S.61, I.62, P.63, G.64, I.65 Ligands: DG-DC-DC-DG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.61

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.6: 18 residues within 4Å: Chain A: R.146, G.176, S.177, R.180, C.185, G.186, 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.1, CA.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.265 Hydrogen bonds: A:S.177, A:S.177, A:G.186, A:D.187, A:N.268 Water bridges: A:R.146, A:Y.178, A:Y.178, A:R.180, A:D.187 Salt bridges: A:R.146, A:R.180

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

EDO.7: 6 residues within 4Å: Chain A: R.201, G.202, I.203, F.204, S.205, R.206 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.204, A:S.205, A:S.205 Water bridges: A:R.201, A:R.201, A:I.203, A:E.225 EDO.8: 4 residues within 4Å: Chain A: S.99, N.100, F.143, L.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.100 EDO.9: 6 residues within 4Å: Chain A: F.254, A.255, L.258, P.309, T.310, E.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.311 Water bridges: A:E.311, A:K.312 EDO.10: 3 residues within 4Å: Chain A: T.226, H.285 Chain B: A.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.226, A:T.226 EDO.11: 3 residues within 4Å: Chain A: V.292, V.300, G.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.300 EDO.12: 4 residues within 4Å: Chain A: S.91, L.95, Q.110, Y.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.91, A:Q.110 Water bridges: A:Y.113 EDO.13: 4 residues within 4Å: Chain B: T.10, G.11 Ligands: DC-DA-DG-DT-DA-DC.1, DC-DA-DG-DT-DA-DC.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nourisson, A. et al., DNA Polymerase Lambda I493R, 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