SMTL ID : 6n9u.1

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) interacting with primase domains of two gp4 subunits bound to an RNA/DNA hybrid and dTTP (from LagS1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

1 x A- C- C- A- G- DOC: RNA (5'-R(*AP*CP*CP*AP*G)-D(P*(DOC))-3')(Non-covalent)

A-C-C-A-G-DOC.1: 24 residues within 4Å: Chain A: Y.37, V.38 Chain C: R.339, V.363, V.364, D.365, D.366, K.394, R.429, A.438, Q.439, I.440, P.441, G.442, R.444, H.653, D.654 Chain D: G.7, C.8, T.9, G.10, G.11, T.12 Ligands: TTP.3 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.654 Hydrogen bonds: C:R.429, C:R.444

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.17, C.20, C.36, C.39 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.17, A:C.20, A:C.36, A:C.39

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.3: 15 residues within 4Å: Chain C: D.475, A.476, S.477, G.478, L.479, E.480, H.506, R.518, K.522, Y.526, D.654 Chain D: A.6, G.7 Ligands: A-C-C-A-G-DOC.1, MG.4 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:E.480, C:Y.526 Hydrogen bonds: C:S.477, C:G.478, C:L.479, C:E.480 Salt bridges: C:H.506, C:R.518, C:K.522, C:K.522, C:K.522 pi-Stacking: C:Y.526

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain C: D.475, A.476, D.654 Ligands: TTP.3 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.475, C:D.475, C:A.476, C:D.654 MG.5: 1 residues within 4Å: Chain C: H.59 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., Structures and operating principles of the replisome. Science (2019)

Release Date

2019-03-06

Peptides

DNA primase/helicase: AB
DNA-directed DNA polymerase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
H

DNA primase/helicase

DNA-directed DNA polymerase

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