SMTL ID : 3hwt.1

Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate with a scrunched dA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DT- DA- 2DT: 5'-D(*CP*AP*GP*TP*AP*(2DT))-3'(Non-covalent)

DC-DA-DG-DT-DA-2DT.1: 22 residues within 4Å: Chain A: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, K.232, L.234, R.248, D.250, Y.265 Chain B: A.6, A.7, T.8, A.9, C.10, T.11, G.12 Ligands: D3T.3, NA.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.232, A:R.248 Water bridges: A:Y.265

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

DG-DC-DC-DG.2: 14 residues within 4Å: Chain A: W.34, R.35, G.38, Y.39, P.63, G.64, I.65, G.66, R.68, M.69 Chain B: C.1, G.2, G.3, C.4 Protein-ligand interaction information (PLIP) not available

1 x D3T: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

D3T.3: 16 residues within 4Å: Chain A: R.146, G.176, S.177, R.180, C.185, G.186, D.187, D.189, Y.265, F.266, G.268, A.270, N.273 Chain B: A.6 Ligands: DC-DA-DG-DT-DA-2DT.1, MG.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.270 Hydrogen bonds: A:S.177, A:S.177, A:S.177, A:G.186, A:D.187, A:N.273 Water bridges: A:R.146, A:R.146, A:R.180, A:R.180, A:R.180, A:R.248, A:R.248, A:R.248, A:R.248 Salt bridges: A:R.146, A:R.180

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.187, D.189 Ligands: D3T.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.187, A:D.189, H2O.3

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

NA.5: 5 residues within 4Å: Chain A: S.99, I.101, G.103, A.104 Ligands: DC-DA-DG-DT-DA-2DT.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.103, A:A.104

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 1 residues within 4Å: Chain A: R.245 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.141, A:S.141, A:D.142, A:R.245, A:R.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Diaz, M. et al., Scrunching during DNA repair synthesis. To be Published

Release Date

2009-08-25

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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