SMTL ID : 1cr2.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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: 5 residues within 4Å: Chain A: R.91, R.93, Q.94, Y.265 Ligands: DTP.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.93, A:Q.94, A:Y.265, A:Y.265 Water bridges: A:L.92 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: 5 residues within 4Å: Chain B: R.91, R.93, Q.94, Y.265 Ligands: DTP.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.93, B:Q.94, B:Y.265, B:Y.265 Water bridges: B:L.92 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: 5 residues within 4Å: Chain C: R.91, R.93, Q.94, Y.265 Ligands: DTP.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.93, C:Q.94, C:Y.265, C:Y.265 Water bridges: C:L.92 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: 5 residues within 4Å: Chain D: R.91, R.93, Q.94, Y.265 Ligands: DTP.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.93, D:Q.94, D:Y.265, D:Y.265 Water bridges: D:L.92 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: DTP.15 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:R.93, E:Q.94, E:Y.265, E:Y.265 Water bridges: E:L.92 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: 5 residues within 4Å: Chain F: R.91, R.93, Q.94, Y.265 Ligands: DTP.18 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:R.93, F:Q.94, F:Y.265, F:Y.265 Water bridges: F:L.92 Salt bridges: F:R.91, F:R.93

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

DTP.3: 20 residues within 4Å: Chain A: G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, R.91, R.93, H.195, R.234, N.242, V.244, Y.265 Chain F: R.252, F.253, T.254, G.255 Ligands: SO4.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:G.45, A:M.46, A:G.47, A:K.48, A:S.49, A:T.50, A:T.50, A:R.91, A:R.234, F:R.252 Water bridges: A:K.48, A:K.48 Salt bridges: A:K.48, A:K.48, A:H.195 pi-Stacking: A:Y.265, A:Y.265 pi-Cation interactions: A:R.234 DTP.6: 20 residues within 4Å: Chain B: G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, R.91, R.93, H.195, R.234, N.242, V.244, Y.265 Chain D: R.252, F.253, T.254, G.255 Ligands: SO4.5 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.45, B:M.46, B:G.47, B:K.48, B:S.49, B:T.50, B:T.50, B:R.91, B:R.234, D:R.252 Water bridges: B:K.48, B:K.48 Salt bridges: B:K.48, B:K.48, B:H.195 pi-Stacking: B:Y.265, B:Y.265 pi-Cation interactions: B:R.234 DTP.9: 20 residues within 4Å: Chain C: G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, R.91, R.93, H.195, R.234, N.242, V.244, Y.265 Chain E: R.252, F.253, T.254, G.255 Ligands: SO4.8 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.45, C:M.46, C:G.47, C:K.48, C:S.49, C:T.50, C:T.50, C:R.91, C:R.234, E:R.252 Water bridges: C:K.48, C:K.48 Salt bridges: C:K.48, C:K.48, C:H.195 pi-Stacking: C:Y.265, C:Y.265 pi-Cation interactions: C:R.234 DTP.12: 20 residues within 4Å: Chain C: R.252, F.253, T.254, G.255 Chain D: G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, R.91, R.93, H.195, R.234, N.242, V.244, Y.265 Ligands: SO4.11 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.45, D:M.46, D:G.47, D:K.48, D:S.49, D:T.50, D:T.50, D:R.91, D:R.234, C:R.252 Water bridges: D:K.48, D:K.48 Salt bridges: D:K.48, D:K.48, D:H.195 pi-Stacking: D:Y.265, D:Y.265 pi-Cation interactions: D:R.234 DTP.15: 16 residues within 4Å: Chain E: G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, R.91, R.93, H.195, R.234, N.242, V.244, Y.265 Ligands: SO4.14 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:G.45, E:M.46, E:G.47, E:K.48, E:S.49, E:T.50, E:T.50, E:R.91, E:R.234 Water bridges: E:K.48, E:K.48 Salt bridges: E:K.48, E:K.48, E:H.195 pi-Stacking: E:Y.265, E:Y.265 pi-Cation interactions: E:R.234 DTP.18: 20 residues within 4Å: Chain B: R.252, F.253, T.254, G.255 Chain F: G.43, S.44, G.45, M.46, G.47, K.48, S.49, T.50, R.91, R.93, H.195, R.234, N.242, V.244, Y.265 Ligands: SO4.17 18 PLIP interactions: 17 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:G.45, F:M.46, F:G.47, F:K.48, F:S.49, F:T.50, F:T.50, F:R.91, F:R.234, B:R.252 Water bridges: F:K.48, F:K.48 Salt bridges: F:K.48, F:K.48, F:H.195 pi-Stacking: F:Y.265, 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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