SMTL ID : 6lel.1

Structure of E. coli beta-glucuronidase complex with C6-hexyl uronic isofagomine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x E8X: (2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid(Non-covalent)

E8X.1: 15 residues within 4Å: Chain A: D.164, H.331, L.362, N.413, E.414, M.448, Y.469, Y.473, E.505, W.550, F.555, R.563, N.567, K.569 Chain D: F.366 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.362, A:Y.469, A:Y.473, A:Y.473, D:F.366, D:F.366 Hydrogen bonds: A:D.164, A:D.164, A:E.505, A:W.550, A:N.567 Salt bridges: A:R.563, A:K.569 E8X.2: 14 residues within 4Å: Chain B: D.164, H.331, L.362, E.414, M.448, Y.469, Y.473, E.505, W.550, F.555, R.563, N.567, K.569 Chain C: F.366 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.362, B:Y.469, B:Y.469, B:Y.473, B:Y.473, B:Y.473, C:F.366 Hydrogen bonds: B:D.164, B:E.505, B:W.550, B:N.567 Salt bridges: B:R.563, B:K.569 E8X.3: 15 residues within 4Å: Chain B: F.366 Chain C: D.164, H.331, L.362, N.413, E.414, M.448, Y.469, Y.473, E.505, W.550, F.555, R.563, N.567, K.569 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.362, C:Y.469, C:Y.473, C:Y.473, B:F.366, B:F.366 Hydrogen bonds: C:D.164, C:Y.473, C:E.505, C:W.550, C:N.567 Salt bridges: C:R.563, C:K.569 E8X.4: 14 residues within 4Å: Chain A: F.366 Chain D: D.164, H.331, L.362, E.414, M.448, Y.469, Y.473, E.505, W.550, F.555, R.563, N.567, K.569 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.362, D:Y.469, D:Y.469, D:Y.473, D:Y.473, D:Y.473, A:F.366 Hydrogen bonds: D:D.164, D:D.164, D:Y.469, D:Y.473, D:E.505, D:W.550, D:N.567 Salt bridges: D:R.563, D:K.569

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, H.Y. et al., Entropy-driven binding of gut bacterial beta-glucuronidase inhibitors ameliorates irinotecan-induced toxicity. Commun Biol (2021)

Release Date

2021-01-27

Peptides

Beta-D-glucuronidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Beta-D-glucuronidase

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