SMTL ID : 2dpj.1

structure of hPoli with DNA and dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x DA- DG- DG- DA- DC- DC- DOC: 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: L.123, G.124, E.127, K.207, P.240, G.241, I.242, G.243, Y.244, K.245, T.246, E.358, S.359, R.360 Ligands: DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, MG.4, TTP.5, DA-DG-DG-DA-DC-DC-DOC.6, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7 Protein-ligand interaction information (PLIP) not available DA-DG-DG-DA-DC-DC-DOC.6: 26 residues within 4Å: Chain B: L.123, G.124, E.127, K.207, P.240, G.241, I.242, G.243, Y.244, K.245, T.246, E.358, S.359, R.360 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7, MG.9, TTP.10 Protein-ligand interaction information (PLIP) not available

2 x DT- EDA- DG- DG- DG- DT- DC- DC- DT: 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3'(Non-covalent)

DT-EDA-DG-DG-DG-DT-DC-DC-DT.2: 32 residues within 4Å: Chain A: Q.59, K.60, Y.61, L.62, V.64, N.80, E.97, L.99, R.103, P.299, Q.300, S.301, F.302, S.303, E.304, E.305, S.307, K.309, R.331 Chain B: Q.361, C.362, P.363 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, TTP.5, DA-DG-DG-DA-DC-DC-DOC.6, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7 Protein-ligand interaction information (PLIP) not available DT-EDA-DG-DG-DG-DT-DC-DC-DT.7: 32 residues within 4Å: Chain A: Q.361, C.362, P.363 Chain B: Q.59, K.60, Y.61, L.62, V.64, N.80, E.97, L.99, R.103, P.299, Q.300, S.301, F.302, S.303, E.304, E.305, S.307, K.309, R.331 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, DA-DG-DG-DA-DC-DC-DOC.6, DA-DG-DG-DA-DC-DC-DOC.6, DA-DG-DG-DA-DC-DC-DOC.6, DA-DG-DG-DA-DC-DC-DOC.6, DA-DG-DG-DA-DC-DC-DOC.6, DA-DG-DG-DA-DC-DC-DOC.6, DA-DG-DG-DA-DC-DC-DOC.6, TTP.10 Protein-ligand interaction information (PLIP) not available

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.34, L.35, D.126 Ligands: MG.4, TTP.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.34, A:L.35, A:D.126 MG.4: 6 residues within 4Å: Chain A: D.34, D.126, E.127 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, MG.3, TTP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.34, A:E.127, H2O.42 MG.8: 5 residues within 4Å: Chain B: D.34, L.35, D.126 Ligands: MG.9, TTP.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.34, B:L.35, B:D.126 MG.9: 6 residues within 4Å: Chain B: D.34, D.126, E.127 Ligands: DA-DG-DG-DA-DC-DC-DOC.6, MG.8, TTP.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.34, B:E.127, H2O.169

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

TTP.5: 18 residues within 4Å: Chain A: D.34, L.35, D.36, C.37, F.38, Y.39, V.64, T.65, Y.68, R.71, K.77, D.126, K.214 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, DT-EDA-DG-DG-DG-DT-DC-DC-DT.2, MG.3, MG.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.39 Hydrogen bonds: A:L.35, A:C.37, A:F.38, A:Y.39 Water bridges: A:F.125, A:K.214 Salt bridges: A:R.71, A:R.71, A:K.77, A:K.77, A:K.77, A:K.214 TTP.10: 18 residues within 4Å: 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, K.214 Ligands: DA-DG-DG-DA-DC-DC-DOC.6, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7, DT-EDA-DG-DG-DG-DT-DC-DC-DT.7, MG.8, MG.9 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.39 Hydrogen bonds: B:L.35, B:C.37, B:F.38, B:Y.39, B:Y.39, B:T.65, B:Y.68 Water bridges: B:D.36, B:D.36, B:F.125, B:K.214 Salt bridges: B:R.71, B:R.71, B:K.77, B:K.77, B:K.77, B:K.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nair, D.T. et al., Hoogsteen base pair formation promotes synthesis opposite the 1,N(6)-ethenodeoxyadenosine lesion by human DNA polymerase iota. Nat.Struct.Mol.Biol. (2006)

Release Date

2006-07-04

Peptides

DNA polymerase iota: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA polymerase iota

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