SMTL ID : 6n9w.1

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

1 x A- C- C- A- G- DOC: Primer(Non-covalent)

A-C-C-A-G-DOC.1: 22 residues within 4Å: Chain A: Y.37, V.38 Chain G: 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 Chain H: G.7, C.8, T.9, G.10, G.11, T.12 Ligands: TTP.11 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.429, G: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

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

TTP.3: 19 residues within 4Å: Chain A: Q.494, K.520, R.522, T.524, G.525 Chain B: G.315, M.316, G.317, K.318, S.319, T.320, Q.343, H.465, R.504, P.511, N.512, Y.535, K.537 Ligands: MG.4 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.315, B:M.316, B:G.317, B:K.318, B:S.319, B:S.319, B:T.320, B:T.320, B:Q.343, B:P.511, B:N.512, B:K.537 Salt bridges: B:K.318, B:K.318, A:K.520, A:R.522 pi-Stacking: B:Y.535 pi-Cation interactions: B:R.504 TTP.5: 20 residues within 4Å: Chain B: Q.494, K.520, C.521, R.522, F.523, T.524, G.525 Chain C: G.315, M.316, G.317, K.318, S.319, T.320, Q.343, H.465, R.504, P.511, N.512, Y.535 Ligands: MG.6 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:G.315, C:M.316, C:G.317, C:K.318, C:S.319, C:T.320, C:T.320, C:N.512, B:R.522 Salt bridges: C:K.318, C:K.318, C:H.465, B:K.520, B:R.522 pi-Stacking: C:Y.535 pi-Cation interactions: C:R.504 TTP.7: 16 residues within 4Å: Chain C: Q.494, R.522, F.523, T.524, G.525 Chain D: G.315, M.316, G.317, K.318, S.319, T.320, Q.343, H.465, R.504, Y.535 Ligands: MG.8 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.535 Hydrogen bonds: D:G.315, D:M.316, D:G.317, D:K.318, D:S.319, D:T.320, D:Q.343, D:P.511, D:N.512, C:R.522, C:R.522 Salt bridges: D:K.318, D:K.318, C:R.522 pi-Cation interactions: D:R.504 TTP.9: 17 residues within 4Å: Chain D: C.521, R.522, F.523, T.524, G.525 Chain E: G.315, M.316, G.317, K.318, S.319, T.320, Q.343, P.511, N.512, V.514, Y.535 Ligands: MG.10 19 PLIP interactions: 16 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:Y.535 Hydrogen bonds: E:G.315, E:M.316, E:G.317, E:K.318, E:S.319, E:S.319, E:T.320, E:T.320, E:Q.343, E:P.511, E:N.512, D:R.522 Salt bridges: E:K.318, E:K.318, D:K.520, D:R.522 pi-Stacking: E:Y.535 pi-Cation interactions: E:R.504 TTP.11: 15 residues within 4Å: Chain G: D.475, A.476, S.477, G.478, L.479, E.480, H.506, R.518, K.522, Y.526, D.654 Chain H: A.6, G.7 Ligands: A-C-C-A-G-DOC.1, MG.12 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:Y.526 Hydrogen bonds: G:D.475, G:S.477, G:G.478, G:L.479, G:E.480 Salt bridges: G:H.506, G:R.518, G:K.522, G:K.522, G:K.522

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain B: S.319, Q.343 Ligands: TTP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.319 MG.6: 3 residues within 4Å: Chain C: S.319, Q.343 Ligands: TTP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.319 MG.8: 4 residues within 4Å: Chain D: S.319, Q.343, D.424 Ligands: TTP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.319 MG.10: 3 residues within 4Å: Chain E: S.319, Q.343 Ligands: TTP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.319 MG.12: 4 residues within 4Å: Chain G: D.475, A.476, D.654 Ligands: TTP.11 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.475, G:D.475, G:A.476, G:D.654 MG.13: 1 residues within 4Å: Chain G: 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: ABCDEF
DNA-directed DNA polymerase: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

DNA primase/helicase

DNA-directed DNA polymerase

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