SMTL ID : 1cr4.1

CRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF THE GENE 4 PROTEIN OF BACTERIOPHAGE T7: COMPLEX WITH DTDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.134, K.138 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.134, A:K.138 SO4.2: 6 residues within 4Å: Chain A: R.91, R.93, Q.94, Y.265 Chain F: F.253 Ligands: TYD.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.93, A:Q.94 Salt bridges: A:R.91, A:R.93 SO4.4: 2 residues within 4Å: Chain B: R.134, K.138 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.134, B:K.138 SO4.5: 6 residues within 4Å: Chain B: R.91, R.93, Q.94, Y.265 Chain D: F.253 Ligands: TYD.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.93, B:Q.94 Salt bridges: B:R.91, B:R.93 SO4.7: 2 residues within 4Å: Chain C: R.134, K.138 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.134, C:K.138 SO4.8: 6 residues within 4Å: Chain C: R.91, R.93, Q.94, Y.265 Chain E: F.253 Ligands: TYD.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.93, C:Q.94 Salt bridges: C:R.91, C:R.93 SO4.10: 2 residues within 4Å: Chain D: R.134, K.138 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.134, D:K.138 SO4.11: 6 residues within 4Å: Chain C: F.253 Chain D: R.91, R.93, Q.94, Y.265 Ligands: TYD.12 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.93, D:Q.94 Salt bridges: D:R.91, D:R.93 SO4.13: 2 residues within 4Å: Chain E: R.134, K.138 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.134, E:K.138 SO4.14: 5 residues within 4Å: Chain E: R.91, R.93, Q.94, Y.265 Ligands: TYD.15 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.93, E:Q.94 Salt bridges: E:R.91, E:R.93 SO4.16: 2 residues within 4Å: Chain F: R.134, K.138 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.134, F:K.138 SO4.17: 6 residues within 4Å: Chain B: F.253 Chain F: R.91, R.93, Q.94, Y.265 Ligands: TYD.18 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.93, F:Q.94 Salt bridges: F:R.91, F:R.93

6 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.3: 18 residues within 4Å: Chain A: S.42, G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, H.195, R.234, Y.265 Chain F: R.252, F.253, T.254, G.255, D.256 Ligands: SO4.2 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:Y.265 Hydrogen bonds: A:G.45, A:M.46, A:G.47, A:K.48, A:S.49, A:S.49, A:T.50, A:T.50, A:R.91, A:R.234, A:R.234, F:R.252 Salt bridges: A:K.48, A:H.195 pi-Stacking: A:Y.265 pi-Cation interactions: A:R.234 TYD.6: 18 residues within 4Å: Chain B: S.42, G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, H.195, R.234, Y.265 Chain D: R.252, F.253, T.254, G.255, D.256 Ligands: SO4.5 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.265 Hydrogen bonds: B:G.45, B:M.46, B:G.47, B:K.48, B:S.49, B:S.49, B:T.50, B:T.50, B:R.91, B:R.234, B:R.234, D:R.252 Salt bridges: B:K.48, B:H.195 pi-Stacking: B:Y.265 pi-Cation interactions: B:R.234 TYD.9: 18 residues within 4Å: Chain C: S.42, G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, H.195, R.234, Y.265 Chain E: R.252, F.253, T.254, G.255, D.256 Ligands: SO4.8 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:Y.265 Hydrogen bonds: C:G.45, C:M.46, C:G.47, C:K.48, C:S.49, C:S.49, C:T.50, C:T.50, C:R.91, C:R.234, C:R.234, E:R.252 Salt bridges: C:K.48, C:H.195 pi-Stacking: C:Y.265 pi-Cation interactions: C:R.234 TYD.12: 18 residues within 4Å: Chain C: R.252, F.253, T.254, G.255, D.256 Chain D: S.42, G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, H.195, R.234, Y.265 Ligands: SO4.11 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.265 Hydrogen bonds: D:G.45, D:M.46, D:G.47, D:K.48, D:S.49, D:S.49, D:T.50, D:T.50, D:R.91, D:R.234, D:R.234, C:R.252 Salt bridges: D:K.48, D:H.195 pi-Stacking: D:Y.265 pi-Cation interactions: D:R.234 TYD.15: 13 residues within 4Å: Chain E: S.42, G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, H.195, R.234, Y.265 Ligands: SO4.14 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:Y.265 Hydrogen bonds: E:G.45, E:M.46, E:G.47, E:K.48, E:S.49, E:S.49, E:T.50, E:T.50, E:R.91, E:R.234, E:R.234 Salt bridges: E:K.48, E:H.195 pi-Stacking: E:Y.265 pi-Cation interactions: E:R.234 TYD.18: 18 residues within 4Å: Chain B: R.252, F.253, T.254, G.255, D.256 Chain F: S.42, G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, H.195, R.234, Y.265 Ligands: SO4.17 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:Y.265 Hydrogen bonds: F:G.45, F:M.46, F:G.47, F:K.48, F:S.49, F:S.49, F:T.50, F:T.50, F:R.91, F:R.234, F:R.234, B:R.252 Salt bridges: F:K.48, F:H.195 pi-Stacking: F:Y.265 pi-Cation interactions: F:R.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sawaya, M.R. et al., Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7. Cell(Cambridge,Mass.) (1999)

Release Date

1999-11-10

Peptides

DNA PRIMASE/HELICASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

DNA PRIMASE/HELICASE

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