SMTL ID : 6lem.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

hetero-2-2-mer

Ligands

4 x E9O: (2~{S},3~{S},4~{R},5~{R})-2-nonyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid(Non-covalent)

E9O.1: 13 residues within 4Å: Chain A: D.165, H.332, E.415, M.449, F.450, Y.470, Y.474, E.506, W.551, F.556, R.564, N.568, K.570 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:M.449, A:F.450, A:Y.470, A:Y.474 Hydrogen bonds: A:D.165, A:H.332, A:Y.470, A:E.506, A:N.568 Salt bridges: A:R.564, A:K.570 E9O.2: 13 residues within 4Å: Chain B: D.161, H.328, L.359, E.411, M.445, F.446, Y.466, Y.470, E.502, W.547, R.560, N.564, K.566 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:M.445, B:Y.466, B:Y.470, B:Y.470 Hydrogen bonds: B:D.161, B:H.328, B:E.502, B:N.564 Salt bridges: B:R.560, B:K.566 E9O.3: 13 residues within 4Å: Chain C: D.165, H.332, E.415, M.449, F.450, Y.470, Y.474, E.506, W.551, F.556, R.564, N.568, K.570 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:M.449, C:F.450, C:Y.470, C:Y.474 Hydrogen bonds: C:H.332, C:Y.474, C:E.506, C:N.568 Salt bridges: C:R.564, C:K.570 E9O.4: 13 residues within 4Å: Chain D: D.161, H.328, L.359, E.411, M.445, F.446, Y.466, Y.470, E.502, W.547, R.560, N.564, K.566 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:M.445, D:Y.466, D:Y.470, D:Y.470 Hydrogen bonds: D:D.161, D:D.161, D:Y.470, D:E.502, D:N.564 Salt bridges: D:R.560, D:K.566

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: AC
Beta-D-glucuronidase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Beta-D-glucuronidase

Beta-D-glucuronidase

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