SMTL ID : 3gv5.2 (1 other biounit)

Human DNA polymerase iota in complex with T template DNA and incoming ddADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x DG- DT- DG- DG- DA- DT- DG- DA- DG: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'(Non-covalent)

DG-DT-DG-DG-DA-DT-DG-DA-DG.1: 29 residues within 4Å: Chain A: L.123, 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, P.363 Chain B: T.4, C.5, T.6, C.7, A.8, T.9, C.10, C.11, A.12, C.13 Ligands: CA.3, ADI.5 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:L.62, A:L.78, A:E.305 Hydrogen bonds: A:Q.59, A:Y.61, A:Q.300, A:Q.300, A:S.301, A:S.303, A:E.305, A:D.306, A:D.306, A:S.307, A:S.307 Water bridges: A:K.60, A:K.60, A:L.78, A:L.99, A:R.103, A:S.301, A:S.301, A:E.305, A:R.331, A:R.331, A:R.331, A:R.347, A:R.357 Salt bridges: A:K.60, A:R.331, A:R.347, A:R.347

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.34, L.35, D.126 Ligands: CA.3, ADI.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.34, A:L.35, A:D.126, H2O.9 CA.3: 5 residues within 4Å: Chain A: D.34, D.126, E.127 Ligands: DG-DT-DG-DG-DA-DT-DG-DA-DG.1, CA.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.34, A:D.34, A:E.127, H2O.1, H2O.9 CA.4: 1 residues within 4Å: Chain A: Q.144 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: E.304 Chain B: T.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.304, H2O.4, H2O.6, H2O.13

1 x ADI: 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADI.5: 17 residues within 4Å: Chain A: D.34, L.35, D.36, C.37, F.38, V.64, T.65, Y.68, R.71, K.77, L.78, D.126, K.214 Chain B: T.3, T.4 Ligands: DG-DT-DG-DG-DA-DT-DG-DA-DG.1, CA.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.77 Hydrogen bonds: A:C.37, A:F.38, A:Y.68 Water bridges: A:Y.39, A:Y.39, A:K.77, A:K.77 Salt bridges: A:R.71, A:R.71, A:K.77, A:K.77, A:K.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirouac, K.N. et al., Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota. Embo J. (2009)

Release Date

2009-06-02

Peptides

DNA polymerase iota: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

DNA polymerase iota

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