SMTL ID : 3mdc.1

DNA polymerase lambda in complex with dFdCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC.1: 23 residues within 4Å: Chain A: I.91, W.92, G.93, A.94, G.95, T.96, K.97, T.98, D.179, L.224, R.238, D.240, Y.255 Chain B: G.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: GTF.3, NA.5, MG.7 Protein-ligand interaction information (PLIP) not available

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

DG-DC-DC-DG.2: 18 residues within 4Å: Chain A: Y.17, W.24, R.25, G.28, Y.29, I.52, P.53, G.54, I.55, G.56, R.58, M.59, K.62 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.4 Protein-ligand interaction information (PLIP) not available

1 x GTF: 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)(Non-covalent)

GTF.3: 19 residues within 4Å: Chain A: R.136, G.166, S.167, R.170, C.175, G.176, D.177, D.179, Y.255, F.256, T.257, G.258, S.259, A.260, N.263 Chain B: G.5 Ligands: DC-DA-DG-DT-DA-DC.1, MG.7, MG.8 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.260 Hydrogen bonds: A:S.167, A:S.167, A:R.170, A:G.176, A:D.177, A:N.263 Water bridges: A:R.136, A:R.136, A:R.136, A:Y.168, A:Y.168 Salt bridges: A:R.136, A:R.170

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

NA.4: 4 residues within 4Å: Chain A: C.50, I.52, I.55 Ligands: DG-DC-DC-DG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.52 NA.5: 6 residues within 4Å: Chain A: S.89, I.91, W.92, G.93, A.94 Ligands: DC-DA-DG-DT-DA-DC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.89, A:G.93, A:A.94 NA.6: 1 residues within 4Å: Chain A: S.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.213 Water bridges: A:E.215 NA.9: 3 residues within 4Å: Chain A: D.132, R.235, H.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.235, A:H.236 Water bridges: A:R.228

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 6 residues within 4Å: Chain A: D.177, D.179, D.240 Ligands: DC-DA-DG-DT-DA-DC.1, GTF.3, MG.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.177, A:D.179, A:D.240 MG.8: 4 residues within 4Å: Chain A: D.177, D.179 Ligands: GTF.3, MG.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.177, A:D.179, H2O.3

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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