SMTL ID : 6p1h.1

Cryo-EM Structure of DNA Polymerase Delta Holoenzyme

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 8 residues within 4Å: Chain A: K.513, C.1078, C.1081, C.1091, N.1093, C.1096, R.1102 Chain B: L.126 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.1078, A:C.1081, A:C.1091, A:C.1096

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

DCP.2: 16 residues within 4Å: Chain A: F.631, N.632, S.633, L.634, Y.635, P.636, R.696, K.723, N.727, Y.730, D.786 Chain D: C.30 Chain E: G.5, G.6 Ligands: CA.3, CA.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.635 Hydrogen bonds: A:S.633, A:L.634, A:Y.635, A:N.727 Salt bridges: A:R.696, A:K.723, A:K.723

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

CA.3: 5 residues within 4Å: Chain A: D.630, F.631, D.786 Ligands: DCP.2, CA.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.630, A:F.631, A:D.786 CA.4: 4 residues within 4Å: Chain A: D.630, D.786 Ligands: DCP.2, CA.3 No protein-ligand interaction detected (PLIP) CA.5: 4 residues within 4Å: Chain A: D.630, N.632, E.822, E.824 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.822 CA.6: 3 residues within 4Å: Chain A: D.343, I.344, D.542 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.343, A:D.343 CA.7: 1 residues within 4Å: Chain E: G.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jain, R. et al., Cryo-EM structure and dynamics of eukaryotic DNA polymerase delta holoenzyme. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-10-02

Peptides

DNA polymerase delta catalytic subunit: A
DNA polymerase delta small subunit: B
DNA polymerase delta subunit 3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA polymerase delta catalytic subunit

DNA polymerase delta small subunit

DNA polymerase delta subunit 3

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