SMTL ID : 5o8y.1

Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.1: 18 residues within 4Å: Chain A: I.42, N.43, P.46, Y.64, Y.73, H.77, F.78 Chain C: I.42, N.43, Y.64, Y.73, H.77 Chain D: I.42, N.43, P.46, Y.64, Y.73, H.77 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.43, A:Y.64, A:H.77 Hydrophobic interactions: C:H.77 PE4.5: 17 residues within 4Å: Chain B: I.42, N.43, P.46, Y.64, Y.73, H.77, F.78 Chain E: N.43, P.46, Y.64, Y.73, F.78 Chain F: I.42, N.43, P.46, Y.64, Y.73 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:F.78 Hydrogen bonds: E:Y.73

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

SO4.2: 7 residues within 4Å: Chain A: D.56, L.57, S.58, T.87, M.88, K.109 Chain B: E.170 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.57, A:S.58, A:S.58, A:S.58, A:T.87, A:M.88 Water bridges: A:K.109 Salt bridges: A:K.109 SO4.3: 2 residues within 4Å: Chain A: F.17, R.20 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.20 SO4.4: 6 residues within 4Å: Chain A: R.76, H.77 Chain C: R.76, H.77 Chain D: R.76, H.77 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D, 2 interactions with chain C Salt bridges: A:R.76, A:H.77, D:R.76, D:H.77, C:R.76, C:H.77 SO4.6: 10 residues within 4Å: Chain A: E.170 Chain B: H.12, D.56, L.57, S.58, L.86, T.87, M.88, N.89, K.109 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.56, B:L.57, B:S.58, B:T.87, B:M.88, B:N.89, A:E.170 Water bridges: B:S.58, B:S.58 Salt bridges: B:H.12, B:K.109 SO4.7: 4 residues within 4Å: Chain B: T.39, G.61, D.62, K.63 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.39, B:T.39, B:D.62, B:K.63 Water bridges: B:Y.64 SO4.8: 10 residues within 4Å: Chain C: H.12, D.56, L.57, S.58, L.86, T.87, M.88, N.89, K.109 Chain E: E.170 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:L.57, C:S.58, C:S.58, C:L.86, C:M.88, C:N.89 Salt bridges: C:H.12, C:K.109 SO4.9: 7 residues within 4Å: Chain D: H.12, D.56, L.57, S.58, T.87, M.88, K.109 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:L.57, D:S.58, D:S.58, D:S.58, D:T.87, D:M.88 Salt bridges: D:H.12, D:K.109 SO4.10: 8 residues within 4Å: Chain C: L.167 Chain E: H.12, D.56, L.57, S.58, T.87, M.88, K.109 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain E Water bridges: C:E.170, C:E.170 Hydrogen bonds: E:D.56, E:L.57, E:S.58, E:T.87, E:M.88 Salt bridges: E:K.109 SO4.11: 3 residues within 4Å: Chain E: F.17, R.20, K.21 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.20, E:K.21 SO4.12: 9 residues within 4Å: Chain D: E.170 Chain F: H.12, D.56, L.57, S.58, T.87, M.88, N.89, K.109 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:D.56, F:L.57, F:S.58, F:T.87, F:M.88, F:N.89 Salt bridges: F:H.12, F:K.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Casino, P. et al., Conformational dynamism for DNA interaction in the Salmonella RcsB response regulator. Nucleic Acids Res. (2018)

Release Date

2017-11-15

Peptides

Transcriptional regulatory protein RcsB: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
G

E
F

F
H

Transcriptional regulatory protein RcsB

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