SMTL ID : 8d9d.1

Human DNA polymerase-alpha/primase elongation complex II bound to primer/template

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: R.119, C.121, C.122, C.128, C.131 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.121, A:C.122, A:C.128, A:C.131 ZN.4: 4 residues within 4Å: Chain C: C.1283, C.1286, C.1310, C.1315 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.1283, C:C.1286, C:C.1310, C:C.1315 ZN.5: 4 residues within 4Å: Chain C: C.1348, C.1353, C.1371, C.1374 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.1348, C:C.1353, C:C.1371, C:C.1374

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

SF4.2: 8 residues within 4Å: Chain B: P.285, P.286, C.287, C.367, I.370, C.384, C.424, P.444 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.287, B:C.367, B:C.384, B:C.424

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 4 residues within 4Å: Chain C: D.860, F.861, D.1004 Ligands: DTP.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.860, C:F.861, C:D.1004 MG.7: 1 residues within 4Å: Chain E: G.1 No protein-ligand interaction detected (PLIP)

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.6: 14 residues within 4Å: Chain C: D.860, F.861, S.863, L.864, Y.865, R.922, K.950, L.951, N.954, D.1004 Chain E: C.12 Chain F: T.2, G.3 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.865 Hydrogen bonds: C:S.863, C:L.864, C:Y.865, C:N.954 Salt bridges: C:R.922, C:K.950, C:K.950, C:K.950

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, Q. et al., Structures of human primosome elongation complexes. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-04-19

Peptides

DNA primase small subunit: A
DNA primase large subunit: B
DNA polymerase alpha catalytic subunit: C
DNA polymerase alpha subunit B: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

DNA primase small subunit

DNA primase large subunit

DNA polymerase alpha catalytic subunit

DNA polymerase alpha subunit B

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