SMTL ID : 6f9k.1

Tryptophan Repressor TrpR from E.coli with 5-methyl-L-tryptophan as ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

8 x D0Q: 5-methyl-L-tryptophan(Non-covalent)

D0Q.1: 14 residues within 4Å: Chain A: R.54, I.57, V.58, T.81, R.84, G.85, S.88 Chain B: N.40, L.41, M.42, L.43, T.44, P.45 Ligands: SO4.5 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:T.44, A:R.54, A:R.54, A:V.58 Hydrogen bonds: B:L.41, A:S.88 Water bridges: B:R.48, B:R.48, A:R.54, A:R.84, A:R.84 Salt bridges: A:R.84 pi-Cation interactions: A:R.54 D0Q.6: 6 residues within 4Å: Chain A: Q.3, Q.4, S.5, P.6, Y.7 Ligands: D0Q.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.6 Hydrogen bonds: A:Q.3 Water bridges: A:S.5, A:S.5 D0Q.7: 14 residues within 4Å: Chain A: L.43, D.46, E.47, A.50, L.51, R.54 Chain B: L.43, E.47, A.50, L.51, R.54 Ligands: SO4.2, SO4.10, D0Q.15 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.43, A:E.47, B:L.43, B:E.47, B:A.50 Hydrogen bonds: A:R.54, A:R.54 Water bridges: A:A.50, A:A.50 D0Q.8: 5 residues within 4Å: Chain A: E.49 Chain B: Q.3, P.6, Y.7 Ligands: D0Q.14 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.46, B:Y.7 Hydrophobic interactions: B:P.6, B:P.6 D0Q.9: 14 residues within 4Å: Chain A: N.40, L.41, M.42, L.43, T.44, P.45 Chain B: R.54, I.57, V.58, T.81, R.84, G.85, S.88 Ligands: SO4.13 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:T.44, B:R.54, B:R.54, B:V.58 Hydrogen bonds: A:L.41, B:S.88 Water bridges: A:R.48, A:R.48, B:R.54, B:R.84, B:R.84 Salt bridges: B:R.84 pi-Cation interactions: B:R.54 D0Q.14: 6 residues within 4Å: Chain B: Q.3, Q.4, S.5, P.6, Y.7 Ligands: D0Q.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.6 Hydrogen bonds: B:Q.3 Water bridges: B:S.5, B:S.5 D0Q.15: 14 residues within 4Å: Chain A: L.43, E.47, A.50, L.51, R.54 Chain B: L.43, D.46, E.47, A.50, L.51, R.54 Ligands: SO4.2, D0Q.7, SO4.10 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.43, A:E.47, A:A.50, B:L.43, B:E.47 Hydrogen bonds: B:R.54, B:R.54 Water bridges: B:A.50, B:A.50 D0Q.16: 5 residues within 4Å: Chain A: Q.3, P.6, Y.7 Chain B: E.49 Ligands: D0Q.6 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.46, A:Y.7 Hydrophobic interactions: A:P.6, A:P.6

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

SO4.2: 5 residues within 4Å: Chain A: T.44, D.46, E.47 Ligands: D0Q.7, D0Q.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.44, A:E.47, A:E.47 SO4.3: 3 residues within 4Å: Chain A: P.45, R.48 Chain B: R.15 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:R.48, A:R.48, B:R.15, B:R.15, B:R.15 Salt bridges: A:R.48, B:R.15 SO4.4: 6 residues within 4Å: Chain A: Q.14, E.18, R.21 Chain B: R.56, E.74, L.75 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.14, B:E.74 Salt bridges: A:R.21, B:R.56 SO4.5: 4 residues within 4Å: Chain A: R.54, T.81, R.84 Ligands: D0Q.1 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.54, A:R.54, A:R.54, A:R.54, A:A.80, A:R.84 Salt bridges: A:R.84 SO4.10: 5 residues within 4Å: Chain B: T.44, D.46, E.47 Ligands: D0Q.7, D0Q.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.44, B:D.46, B:E.47 SO4.11: 3 residues within 4Å: Chain A: R.15 Chain B: P.45, R.48 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:R.15, A:R.15, A:R.15, B:R.48, B:R.48 Salt bridges: A:R.15, B:R.48 SO4.12: 6 residues within 4Å: Chain A: R.56, E.74, L.75 Chain B: Q.14, E.18, R.21 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.56, B:R.21 Hydrogen bonds: B:Q.14, B:E.18 SO4.13: 4 residues within 4Å: Chain B: R.54, T.81, R.84 Ligands: D0Q.9 7 PLIP interactions: 7 interactions with chain B Water bridges: B:R.54, B:R.54, B:R.54, B:R.54, B:A.80, B:R.84 Salt bridges: B:R.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stiel, A.C. et al., Tryptophan Repressor TrpR from E.coli: A ligand binding study. To Be Published

Release Date

2019-01-30

Peptides

Trp operon repressor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Trp operon repressor

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