SMTL ID : 3fxu.1

Crystal structure of TsaR in complex with its effector p-toluenesulfonate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

22 x TSU: PARA-TOLUENE SULFONATE(Non-covalent)

TSU.1: 3 residues within 4Å: Chain A: R.51, T.52, K.53 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.51, A:K.53 Salt bridges: A:K.53 TSU.2: 2 residues within 4Å: Chain A: K.53, R.54 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.53 Salt bridges: A:K.53, A:R.54 pi-Cation interactions: A:R.54 TSU.3: 8 residues within 4Å: Chain A: S.18, L.19, R.20, R.51, K.53, R.54, G.55, V.56 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.19, A:R.20 Water bridges: A:R.51 Salt bridges: A:R.20 pi-Cation interactions: A:R.51 TSU.4: 16 residues within 4Å: Chain A: S.99, P.100, A.101, M.129, A.148, Y.164, S.166, S.196, A.197, I.204, F.226, P.243, P.268, I.270 Ligands: TSU.5, GOL.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.148, A:A.197, A:I.204, A:F.226, A:P.243, A:P.268 Hydrogen bonds: A:S.99, A:S.99, A:A.101, A:A.148, A:S.166 TSU.5: 7 residues within 4Å: Chain A: A.101, S.166, D.167, P.243, R.244, T.245 Ligands: TSU.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.101, A:D.167, A:P.243, A:R.244, A:T.245 Hydrogen bonds: A:D.167 TSU.6: 6 residues within 4Å: Chain A: A.149, H.150, P.266, N.267, P.268, T.269 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.266, A:P.268 Hydrogen bonds: A:T.269 Salt bridges: A:H.150 pi-Stacking: A:H.150 TSU.12: 11 residues within 4Å: Chain B: S.99, P.100, A.101, M.129, A.148, S.196, I.204, F.226, P.243, P.268, I.270 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.148, B:I.204, B:F.226, B:P.243, B:P.268 Hydrogen bonds: B:S.99, B:A.101, B:A.148 TSU.13: 8 residues within 4Å: Chain B: A.101, I.102, A.105, Y.164, S.166, D.167, R.244, T.245 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.101, B:I.102, B:A.105, B:Y.164, B:Y.164 Hydrogen bonds: B:D.167, B:R.244, B:T.245 TSU.14: 4 residues within 4Å: Chain B: S.113, R.116, E.117, W.290 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.116, B:E.117, B:W.290, B:W.290 Water bridges: B:S.113, B:R.116 Salt bridges: B:R.116 TSU.15: 9 residues within 4Å: Chain B: R.191, G.220, L.221, S.236, D.237, L.238 Chain C: L.111, A.115, V.123 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.221, B:L.238, B:L.238, C:L.111, C:A.115, C:V.123 Hydrogen bonds: B:D.237 Salt bridges: B:R.191 TSU.16: 3 residues within 4Å: Chain B: H.152, D.153, R.199 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:H.152 Salt bridges: B:H.152, B:R.199 TSU.21: 3 residues within 4Å: Chain C: R.51, T.52, K.53 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.51, C:K.53 Salt bridges: C:K.53 TSU.22: 2 residues within 4Å: Chain C: K.53, R.54 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.53 Salt bridges: C:K.53, C:R.54 pi-Cation interactions: C:R.54 TSU.23: 8 residues within 4Å: Chain C: S.18, L.19, R.20, R.51, K.53, R.54, G.55, V.56 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.19, C:R.20 Water bridges: C:R.51 Salt bridges: C:R.20 pi-Cation interactions: C:R.51 TSU.24: 16 residues within 4Å: Chain C: S.99, P.100, A.101, M.129, A.148, Y.164, S.166, S.196, A.197, I.204, F.226, P.243, P.268, I.270 Ligands: TSU.25, GOL.28 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:A.148, C:A.197, C:I.204, C:F.226, C:P.243, C:P.268 Hydrogen bonds: C:S.99, C:S.99, C:A.101, C:A.148, C:Y.164, C:S.166 TSU.25: 7 residues within 4Å: Chain C: A.101, S.166, D.167, P.243, R.244, T.245 Ligands: TSU.24 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.101, C:D.167, C:P.243, C:R.244, C:T.245 Hydrogen bonds: C:D.167 TSU.26: 6 residues within 4Å: Chain C: A.149, H.150, P.266, N.267, P.268, T.269 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.266, C:P.268 Hydrogen bonds: C:T.269, C:T.269 Salt bridges: C:H.150 pi-Stacking: C:H.150 TSU.32: 11 residues within 4Å: Chain D: S.99, P.100, A.101, M.129, A.148, S.196, I.204, F.226, P.243, P.268, I.270 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.148, D:I.204, D:F.226, D:P.243, D:P.268 Hydrogen bonds: D:S.99, D:A.101, D:A.148 TSU.33: 8 residues within 4Å: Chain D: A.101, I.102, A.105, Y.164, S.166, D.167, R.244, T.245 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:A.101, D:I.102, D:A.105, D:Y.164, D:Y.164 Hydrogen bonds: D:Y.164, D:D.167, D:R.244, D:T.245, D:T.245 TSU.34: 4 residues within 4Å: Chain D: S.113, R.116, E.117, W.290 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:R.116, D:E.117, D:W.290, D:W.290 Water bridges: D:S.113, D:R.116 Salt bridges: D:R.116 TSU.35: 9 residues within 4Å: Chain A: L.111, A.115, V.123 Chain D: R.191, G.220, L.221, S.236, D.237, L.238 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:L.111, A:A.115, A:V.123, D:L.221, D:L.238, D:L.238 Hydrogen bonds: D:D.237 Salt bridges: D:R.191 TSU.36: 3 residues within 4Å: Chain D: H.152, D.153, R.199 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:H.152 Salt bridges: D:H.152, D:R.199

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 6 residues within 4Å: Chain A: A.98, S.99, P.100, D.127, G.128 Chain D: L.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.98 IMD.27: 6 residues within 4Å: Chain B: L.227 Chain C: A.98, S.99, P.100, D.127, G.128 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.98, C:D.127

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: F.194, S.195, S.196, A.197, G.202, A.203, I.204, I.205, T.241 Ligands: TSU.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.195, A:S.195, A:G.202, A:I.204 GOL.9: 10 residues within 4Å: Chain A: L.227, P.230, N.250, A.251, F.252 Chain D: L.104, L.246, R.249, N.250, A.251 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:A.251, D:A.251 Water bridges: A:L.227, A:G.231 GOL.10: 1 residues within 4Å: Chain A: A.185 No protein-ligand interaction detected (PLIP) GOL.17: 3 residues within 4Å: Chain B: W.90, E.117, F.118 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.117 Water bridges: B:W.90, B:F.118 GOL.28: 10 residues within 4Å: Chain C: F.194, S.195, S.196, A.197, G.202, A.203, I.204, I.205, T.241 Ligands: TSU.24 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.195, C:S.195, C:G.202, C:I.204 GOL.29: 10 residues within 4Å: Chain B: L.104, L.246, R.249, N.250, A.251 Chain C: L.227, P.230, N.250, A.251, F.252 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.251, B:A.251 Water bridges: C:L.227, C:G.231 GOL.30: 1 residues within 4Å: Chain C: A.185 No protein-ligand interaction detected (PLIP) GOL.37: 3 residues within 4Å: Chain D: W.90, E.117, F.118 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.117, D:E.117 Water bridges: D:W.90, D:F.118

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 3 residues within 4Å: Chain A: E.41, A.46, P.47 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain B: R.289 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: H.150, A.197, P.198, R.199 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain C: E.41, A.46, P.47 Ligand excluded by PLIP CL.39: 1 residues within 4Å: Chain D: R.289 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain D: H.150, A.197, P.198, R.199 Ligand excluded by PLIP

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.18: 5 residues within 4Å: Chain A: L.2, K.3 Chain B: K.3, L.4, Q.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.4, B:Q.5, A:K.3 Water bridges: A:L.4 FMT.38: 5 residues within 4Å: Chain C: L.2, K.3 Chain D: K.3, L.4, Q.5 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.3, D:L.4, D:Q.5 Water bridges: C:L.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Monferrer, D. et al., Structural studies on the full-length LysR-type regulator TsaR from Comamonas testosteroni T-2 reveal a novel open conformation of the tetrameric LTTR fold. Mol.Microbiol. (2010)

Release Date

2010-01-26

Peptides

LysR type regulator of tsaMBCD: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

LysR type regulator of tsaMBCD

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