SMTL ID : 6n7v.1

Structure of bacteriophage T7 gp4 (helicase-primase, E343Q mutant) in complex with ssDNA, dTTP, AC dinucleotide, and CTP (from multiple lead complexes)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

TTP.1: 21 residues within 4Å: Chain A: K.520, C.521, R.522, T.524, G.525 Chain B: G.313, G.315, M.316, G.317, K.318, S.319, T.320, Q.343, H.465, R.504, P.511, N.512, V.514, Y.535, L.542 Ligands: MG.2 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.535, B:L.542 Hydrogen bonds: B:G.315, B:M.316, B:G.317, B:K.318, B:S.319, B:T.320, B:T.320, B:T.320, B:Q.343, B:R.504, B:P.511 Salt bridges: B:K.318, B:K.318, B:H.465, A:K.520, A:R.522 pi-Stacking: B:Y.535 pi-Cation interactions: B:R.504 TTP.3: 20 residues within 4Å: Chain B: K.520, R.522, F.523, T.524, G.525 Chain C: G.315, M.316, G.317, K.318, S.319, T.320, Q.343, R.361, H.465, R.504, P.511, N.512, Y.535, K.537 Ligands: MG.4 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Y.535 Hydrogen bonds: C:G.315, C:M.316, C:G.317, C:K.318, C:S.319, C:S.319, C:T.320, C:T.320, C:R.361, C:N.512, B:R.522 Salt bridges: C:H.465, B:K.520, B:R.522 pi-Stacking: C:Y.535 pi-Cation interactions: C:R.504 TTP.5: 19 residues within 4Å: Chain C: K.520, 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, P.511, N.512, V.514, Y.535, K.537 Ligands: MG.6 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.315, D:M.316, D:G.317, D:K.318, D:S.319, D:T.320, D:T.320, D:Q.343, D:P.511, D:K.537, C:R.522 Salt bridges: D:K.318, D:K.318, D:H.465, C:K.520, C:R.522 pi-Stacking: D:Y.535 pi-Cation interactions: D:R.504 TTP.7: 17 residues within 4Å: Chain D: C.521, R.522, G.525 Chain E: S.314, G.315, M.316, G.317, K.318, S.319, T.320, Q.343, H.465, N.512, V.514, Y.535, K.537 Ligands: MG.8 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain D 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:N.512, E:K.537 Salt bridges: E:K.318, E:K.318, E:H.465, D:K.520, D:R.522 pi-Stacking: E:Y.535 pi-Cation interactions: E:R.504 TTP.9: 20 residues within 4Å: Chain E: Q.494, C.521, R.522, T.524, G.525 Chain F: G.313, S.314, G.315, M.316, G.317, K.318, S.319, T.320, Q.343, H.465, R.504, P.511, N.512, K.537 Ligands: MG.10 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.315, F:G.317, F:K.318, F:S.319, F:S.319, F:S.319, F:T.320, F:T.320, F:N.512, F:K.537 Salt bridges: F:K.318, F:K.318, F:H.465, E:K.520, E:R.522 pi-Stacking: F:Y.535 pi-Cation interactions: F:R.504

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: S.319, Q.343 Ligands: TTP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.319 MG.4: 3 residues within 4Å: Chain C: S.319, Q.343 Ligands: TTP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.319 MG.6: 3 residues within 4Å: Chain D: S.319, Q.343 Ligands: TTP.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.319 MG.8: 4 residues within 4Å: Chain E: K.318, S.319, Q.343 Ligands: TTP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.319 MG.10: 5 residues within 4Å: Chain F: K.318, S.319, Q.343, D.424 Ligands: TTP.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.319

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DNA primase/helicase

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