SMTL ID : 9ddr.1

Ternary substrate complex of DNA polymerase iota with DNA (template A), Ca2+, and dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

TTP.1: 20 residues within 4Å: Chain A: D.34, L.35, D.36, C.37, F.38, Y.39, A.40, V.64, T.65, Y.68, R.71, K.77, L.78, D.126, K.214 Chain B: C.18 Chain D: A.4, G.5 Ligands: CA.2, CA.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.39 Hydrogen bonds: A:L.35, A:C.37, A:F.38, A:Y.39, A:Y.39, A:Y.68 Water bridges: A:K.77, A:K.77, A:K.77, A:K.77, A:F.125 Salt bridges: A:R.71, A:R.71, A:K.77, A:K.77, A:K.77, A:K.214 TTP.4: 20 residues within 4Å: Chain B: A.4, G.5 Chain C: D.34, L.35, D.36, C.37, F.38, Y.39, A.40, V.64, T.65, Y.68, R.71, K.77, L.78, D.126, K.214 Chain D: C.18 Ligands: CA.5, CA.6 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:Y.39 Hydrogen bonds: C:L.35, C:C.37, C:F.38, C:Y.39, C:Y.39, C:Y.68 Water bridges: C:K.77, C:K.77, C:K.77, C:K.77, C:F.125 Salt bridges: C:R.71, C:R.71, C:K.77, C:K.77, C:K.77, C:K.214

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.34, L.35, D.126 Ligands: TTP.1, CA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.34, A:L.35, A:D.126 CA.3: 6 residues within 4Å: Chain A: D.34, D.126, E.127 Chain B: C.18 Ligands: TTP.1, CA.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.34, A:D.126, A:D.126, A:E.127 CA.5: 5 residues within 4Å: Chain C: D.34, L.35, D.126 Ligands: TTP.4, CA.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.34, C:L.35, C:D.126 CA.6: 6 residues within 4Å: Chain C: D.34, D.126, E.127 Chain D: C.18 Ligands: TTP.4, CA.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.34, C:D.126, C:D.126, C:E.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frevert, Z. et al., Visualizing DNA polymerase iota catalyze Hoogsteen-directed DNA synthesis. Nat Commun (2025)

Release Date

2025-07-09

Peptides

DNA polymerase iota: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

DNA polymerase iota

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