SMTL ID : 1xsp.1

Crystal Structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC-DG.1: 31 residues within 4Å: Chain A: C.5, G.6, T.7, A.8, C.9, T.10, G.11 Chain B: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, R.180, D.187, D.189, R.248, D.250, Y.265, F.266, T.267, G.268, S.269, A.270, N.273, R.277 Ligands: NA.4, NA.5, PPV.7 Protein-ligand interaction information (PLIP) not available

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

DG-DC-DC-DG.2: 16 residues within 4Å: Chain A: C.1, G.2, G.3, C.4 Chain B: W.34, R.35, G.38, Y.39, P.63, G.64, I.65, G.66, R.68, M.69, K.72 Ligands: NA.3 Protein-ligand interaction information (PLIP) not available

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

NA.3: 2 residues within 4Å: Chain B: K.84 Ligands: DG-DC-DC-DG.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.84, B:K.84 Water bridges: B:R.35 NA.4: 4 residues within 4Å: Chain B: D.187, D.189 Ligands: DC-DA-DG-DT-DA-DC-DG.1, PPV.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.187 Water bridges: B:G.186, B:D.187 NA.5: 6 residues within 4Å: Chain B: S.99, I.101, W.102, G.103, A.104 Ligands: DC-DA-DG-DT-DA-DC-DG.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.101, B:G.103, B:A.104 NA.6: 2 residues within 4Å: Chain A: T.10 Chain B: S.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.223 Water bridges: B:S.223

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.7: 8 residues within 4Å: Chain B: R.146, G.176, S.177, R.180, G.186, D.189 Ligands: DC-DA-DG-DT-DA-DC-DG.1, NA.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.177, B:S.177, B:G.186 Water bridges: B:Y.178, B:D.187, B:D.187, B:D.187, B:R.248 Salt bridges: B:R.146, B:R.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Diaz, M. et al., A closed conformation for the Pol lambda catalytic cycle. Nat.Struct.Mol.Biol. (2005)

Release Date

2005-01-18

Peptides

DNA polymerase lambda: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA polymerase lambda

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