SMTL ID : 2ogg.1

Structure of B. subtilis trehalose repressor (TreR) effector binding domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: H.114 Chain D: H.114 Ligands: NA.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.114 NA.7: 3 residues within 4Å: Chain B: H.114 Chain C: H.114 Ligands: NA.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.114 NA.13: 3 residues within 4Å: Chain B: H.114 Chain C: H.114 Ligands: NA.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.114 NA.19: 3 residues within 4Å: Chain A: H.114 Chain D: H.114 Ligands: NA.1 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.114, A:H.114

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

SO4.2: 8 residues within 4Å: Chain A: R.42, R.44, N.73, S.74, I.75, Y.76 Chain B: K.152 Chain C: L.85 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.75, A:Y.76 Salt bridges: A:R.42, A:R.44, B:K.152 SO4.3: 5 residues within 4Å: Chain A: D.34, D.35, D.36, R.60, K.61 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.34, A:D.35, A:D.36, A:D.36 Water bridges: A:R.60, A:K.61 Salt bridges: A:R.60 SO4.8: 8 residues within 4Å: Chain A: K.152 Chain B: R.42, R.44, N.73, S.74, I.75, Y.76 Chain D: L.85 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.75, B:Y.76 Salt bridges: B:R.42, B:R.44, A:K.152 SO4.9: 5 residues within 4Å: Chain B: D.34, D.35, D.36, R.60, K.61 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.34, B:D.36 Water bridges: B:R.60, B:K.61 Salt bridges: B:R.60 SO4.14: 8 residues within 4Å: Chain A: L.85 Chain C: R.42, R.44, N.73, S.74, I.75, Y.76 Chain D: K.152 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.75, C:Y.76 Salt bridges: C:R.42, C:R.44, D:K.152 SO4.15: 5 residues within 4Å: Chain C: D.34, D.35, D.36, R.60, K.61 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.34, C:D.35, C:D.36, C:D.36 Water bridges: C:R.60, C:K.61 Salt bridges: C:R.60 SO4.20: 8 residues within 4Å: Chain B: L.85 Chain C: K.152 Chain D: R.42, R.44, N.73, S.74, I.75, Y.76 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:I.75, D:Y.76 Salt bridges: D:R.42, D:R.44, C:K.152 SO4.21: 5 residues within 4Å: Chain D: D.34, D.35, D.36, R.60, K.61 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.34, D:D.36 Water bridges: D:R.60, D:K.61 Salt bridges: D:R.60

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: G.17, E.19, P.20, P.21, S.22, I.25, I.37, E.39 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.19, A:S.22, A:S.22, A:I.37 Water bridges: A:E.39 GOL.5: 5 residues within 4Å: Chain A: L.29, R.30, F.59, S.128, L.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.30, A:R.30, A:L.129 GOL.6: 3 residues within 4Å: Chain A: R.30, Q.91, Y.121 No protein-ligand interaction detected (PLIP) GOL.10: 8 residues within 4Å: Chain B: G.17, E.19, P.20, P.21, S.22, I.25, I.37, E.39 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.19, B:S.22, B:S.22, B:I.37 Water bridges: B:E.19 GOL.11: 5 residues within 4Å: Chain B: L.29, R.30, F.59, S.128, L.129 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.30, B:R.30, B:L.129 GOL.12: 3 residues within 4Å: Chain B: R.30, Q.91, Y.121 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.91 GOL.16: 8 residues within 4Å: Chain C: G.17, E.19, P.20, P.21, S.22, I.25, I.37, E.39 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.19, C:S.22, C:S.22, C:I.37 Water bridges: C:E.39 GOL.17: 5 residues within 4Å: Chain C: L.29, R.30, F.59, S.128, L.129 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.30, C:R.30, C:L.129 GOL.18: 3 residues within 4Å: Chain C: R.30, Q.91, Y.121 No protein-ligand interaction detected (PLIP) GOL.22: 8 residues within 4Å: Chain D: G.17, E.19, P.20, P.21, S.22, I.25, I.37, E.39 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.19, D:S.22, D:S.22, D:I.37 Water bridges: D:E.19 GOL.23: 5 residues within 4Å: Chain D: L.29, R.30, F.59, S.128, L.129 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.30, D:R.30, D:L.129 GOL.24: 3 residues within 4Å: Chain D: R.30, Q.91, Y.121 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rezacova, P. et al., The crystal structure of the effector-binding domain of the trehalose repressor TreR from Bacillus subtilis 168 reveals a unique quarternary assembly. Proteins (2007)

Release Date

2007-02-06

Peptides

Trehalose operon transcriptional repressor: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Trehalose operon transcriptional repressor