SMTL ID : 3mda.1

DNA polymerase lambda in complex with araC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC-CAR.1: 32 residues within 4Å: Chain A: I.91, W.92, G.93, A.94, G.95, T.96, K.97, T.98, G.166, R.170, D.177, D.179, L.224, R.238, D.240, Y.255, F.256, T.257, G.258, S.259, A.260, N.263 Chain B: G.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: PPV.3, NA.4, MG.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.170, A:D.240, A:S.259, A:N.263 Water bridges: A:A.260

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

DG-DC-DC-DG.2: 16 residues within 4Å: Chain A: Y.17, W.24, R.25, G.28, Y.29, P.53, G.54, I.55, G.56, R.58, M.59, K.62 Chain B: C.1, G.2, G.3, C.4 Protein-ligand interaction information (PLIP) not available

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3: 10 residues within 4Å: Chain A: R.136, G.166, S.167, R.170, C.175, G.176, D.177, D.179 Ligands: DC-DA-DG-DT-DA-DC-CAR.1, MG.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.167, A:S.167, A:S.167, A:G.176, A:D.177 Water bridges: A:Y.168, A:Y.168, A:R.170, A:R.170, A:R.238 Salt bridges: A:R.136, A:R.170

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

NA.4: 6 residues within 4Å: Chain A: S.89, I.91, W.92, G.93, A.94 Ligands: DC-DA-DG-DT-DA-DC-CAR.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.93, A:A.94, A:A.94 NA.5: 2 residues within 4Å: Chain A: S.213 Chain B: T.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.213 Water bridges: A:S.213

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: D.177, D.179 Ligands: DC-DA-DG-DT-DA-DC-CAR.1, PPV.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.177, A:D.179, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Diaz, M. et al., Interaction between DNA Polymerase lambda and anticancer nucleoside analogs. J.Biol.Chem. (2010)

Release Date

2010-04-28

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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