SMTL ID : 4ptf.1

Ternary crystal structure of yeast DNA polymerase epsilon with template G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

monomer

Ligands

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.1: 19 residues within 4Å: Chain A: Y.438, D.647, V.648, A.649, S.650, M.651, Y.652, P.653, R.788, K.792, K.831, N.835, Y.838, D.884 Chain B: C.12 Chain C: G.4, G.5 Ligands: CA.2, CA.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.652 Hydrogen bonds: A:Y.438, A:Y.438, A:S.650, A:M.651, A:Y.652, A:N.835, A:N.835 Water bridges: A:D.647, A:R.788, A:K.792, A:K.831, A:E.952 Salt bridges: A:R.788, A:R.788, A:K.792, A:K.831, A:K.831, A:K.831

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 5 residues within 4Å: Chain A: D.647, V.648, D.884 Ligands: DCP.1, CA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.647, A:V.648, A:D.884 CA.3: 5 residues within 4Å: Chain A: D.647, D.884 Chain B: C.12 Ligands: DCP.1, CA.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.647, A:D.884 CA.4: 2 residues within 4Å: Chain A: D.297, D.390 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.297, H2O.3 CA.6: 1 residues within 4Å: Chain C: G.9 No protein-ligand interaction detected (PLIP)

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

NA.5: 4 residues within 4Å: Chain A: R.975, F.991, K.1163 Chain C: G.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.975, A:E.992

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

EDO.7: 5 residues within 4Å: Chain B: T.2, C.3 Chain C: A.12, G.13, G.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jain, R. et al., Crystal Structure of Yeast DNA Polymerase epsilon Catalytic Domain. Plos One (2014)

Release Date

2014-04-30

Peptides

DNA polymerase epsilon catalytic subunit A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase epsilon catalytic subunit A