SMTL ID : 1xsn.1

Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddTTP

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: 24 residues within 4Å: Chain A: A.5, A.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, L.234, R.248, D.250, Y.265 Ligands: EDO.4, EDO.5, EDO.6, NA.8, D3T.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.248 Water bridges: B:K.232, B:K.232

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

DG-DC-DC-DG.2: 15 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 Protein-ligand interaction information (PLIP) not available

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

EDO.3: 1 residues within 4Å: Chain A: C.1 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain B: T.108, M.111 Ligands: DC-DA-DG-DT-DA-2DT.1 No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Ligands: DC-DA-DG-DT-DA-2DT.1, DC-DA-DG-DT-DA-2DT.1 No protein-ligand interaction detected (PLIP) EDO.6: 2 residues within 4Å: Ligands: DC-DA-DG-DT-DA-2DT.1, DC-DA-DG-DT-DA-2DT.1 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain B: D.187, D.189 Ligands: D3T.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:D.189, H2O.4

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

NA.8: 5 residues within 4Å: Chain B: S.99, I.101, G.103, A.104 Ligands: DC-DA-DG-DT-DA-2DT.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.99, B:G.103, B:A.104 NA.9: 2 residues within 4Å: Chain A: T.10 Chain B: S.223 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.223, B:S.223

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

D3T.10: 16 residues within 4Å: Chain A: A.5 Chain B: 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 Ligands: DC-DA-DG-DT-DA-2DT.1, MG.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.270 Hydrogen bonds: B:S.177, B:S.177, B:S.177, B:G.186, B:D.187, B:N.273 Water bridges: B:R.180, B:R.180, B:R.180, B:R.248, 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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