SMTL ID : 4q2u.2 (3 other biounits)

Crystal structure of the E. coli DinJ-YafQ toxin-antitoxin complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-oligomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: N.55, Q.56 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.56 Water bridges: A:N.55, A:N.55, A:L.57 SO4.2: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.32 SO4.3: 4 residues within 4Å: Chain A: A.5, F.6, R.8 Chain C: K.16 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A Water bridges: C:K.16, C:K.16, A:R.8, A:R.8, A:R.8 Salt bridges: C:K.16, A:R.8 Hydrogen bonds: A:F.6 SO4.4: 4 residues within 4Å: Chain A: S.31, R.35 Chain C: A.9, R.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.31, A:S.31, C:R.10 Salt bridges: A:R.35 SO4.5: 4 residues within 4Å: Chain B: P.61, R.70 Chain D: P.61, R.70 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Salt bridges: B:R.70, D:R.70 SO4.6: 4 residues within 4Å: Chain A: E.66 Chain B: K.83, L.88, R.90 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.17 Salt bridges: B:K.83, B:R.90 SO4.7: 8 residues within 4Å: Chain A: P.48, F.49, D.50 Chain B: H.60, D.71, H.73, H.97, F.101 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:D.71, A:P.48, A:D.50, A:D.50 Salt bridges: B:H.60, B:H.73, B:H.97 Water bridges: A:L.51, A:L.51, A:L.51, A:L.51, A:R.52 SO4.8: 2 residues within 4Å: Chain B: P.54, A.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.55 SO4.9: 4 residues within 4Å: Chain B: R.32, T.96, A.98, A.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.96 Water bridges: B:R.32 Salt bridges: B:R.32 SO4.10: 4 residues within 4Å: Chain A: R.52, E.53 Chain C: R.43 Ligands: SO4.1 9 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 6 interactions with chain C Hydrogen bonds: A:E.53 Water bridges: A:E.53, B:F.101, C:R.43, C:R.43, C:R.43, C:R.43, C:R.43 Salt bridges: C:R.43 SO4.11: 9 residues within 4Å: Chain C: P.48, F.49, D.50 Chain D: H.60, D.71, H.73, I.79, H.97, F.101 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:D.50 Water bridges: C:L.51, C:L.51, C:L.51, C:R.52, D:D.71 Salt bridges: D:H.60, D:H.73, D:H.97 SO4.12: 2 residues within 4Å: Chain D: R.32, K.34 5 PLIP interactions: 5 interactions with chain D Water bridges: D:K.34, D:K.34, D:E.75 Salt bridges: D:R.32, D:K.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruangprasert, A. et al., Mechanisms of Toxin Inhibition and Transcriptional Repression by Escherichia coli DinJ-YafQ. J.Biol.Chem. (2014)

Release Date

2014-06-11

Peptides

Antitoxin DinJ: AC
mRNA interferase YafQ: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
K

B
D

D
L

Antitoxin DinJ

mRNA interferase YafQ

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