SMTL ID : 8ucv.1

Complete DNA termination subcomplex 1 of Xenopus laevis DNA polymerase alpha-primase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 21 residues within 4Å: Chain A: D.528, F.529, N.530, S.531, L.532, Y.533, P.534, R.587, K.591, K.615, L.616, N.619, S.620, Y.622, G.623, T.668, D.669 Chain C: C.16, G.17 Chain D: C.29 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.533 Hydrogen bonds: A:N.530, A:S.531, A:L.532, A:Y.533, A:N.619, A:G.623 Salt bridges: A:R.587, A:K.591, A:K.615, A:K.615, A:K.615

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.528, F.529, D.669 Ligands: DGT.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.528, A:F.529, A:D.669 MG.4: 3 residues within 4Å: Chain B: H.309, R.312 Chain D: G.1 No protein-ligand interaction detected (PLIP)

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

SF4.3: 14 residues within 4Å: Chain B: P.291, L.292, C.293, C.373, V.376, C.390, P.391, F.392, Y.426, Q.427, C.430, L.447, P.450, Y.453 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.293, B:C.373, B:C.390, B:C.430

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mullins, E.A. et al., A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase. Nat.Struct.Mol.Biol. (2024)

Release Date

2023-10-11

Peptides

DNA polymerase alpha catalytic subunit: A
DNA primase large subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA polymerase alpha catalytic subunit

DNA primase large subunit

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