SMTL ID : 5ulw.1

Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

monomer

Ligands

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

DA-DG-DG-DA-DC-DC-DOC.1: 26 residues within 4Å: Chain A: A.4, G.5, G.6, G.7, T.8, C.9, C.10, T.11 Chain B: L.123, G.124, D.126, E.127, K.207, I.239, P.240, G.241, I.242, G.243, Y.244, K.245, T.246, E.358, S.359, R.360, Q.361 Ligands: TTP.2 2 PLIP interactions: 2 interactions with chain B Water bridges: B:F.125 Salt bridges: B:K.207

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

TTP.2: 18 residues within 4Å: Chain A: A.4, G.5 Chain B: D.34, L.35, D.36, C.37, F.38, Y.39, V.64, T.65, Y.68, R.71, K.77, D.126, E.127, K.214 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, MG.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.39, B:V.64 Hydrogen bonds: B:L.35, B:C.37, B:F.38, B:Y.39, B:T.65, B:E.127 Water bridges: B:Q.59, B:F.125 Salt bridges: B:R.71, B:R.71, B:K.77, B:K.77, B:K.77, B:K.214

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain B: D.34, L.35, D.126 Ligands: TTP.2 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.34, B:L.35, B:D.126

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain B: N.290 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jain, R. et al., Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-iota. Sci Rep (2017)

Release Date

2017-04-19

Peptides

DNA polymerase iota: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA polymerase iota

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