SMTL ID : 6leg.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x SJ5: (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid(Non-covalent)

SJ5.1: 11 residues within 4Å: Chain A: D.164, H.331, E.414, Y.469, Y.473, E.505, W.550, F.555, R.563, N.567, K.569 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.164, A:H.331, A:Y.469, A:Y.473, A:E.505, A:W.550, A:N.567 Salt bridges: A:R.563, A:K.569 SJ5.2: 12 residues within 4Å: Chain B: D.164, H.331, I.364, E.414, Y.469, Y.473, E.505, W.550, F.555, R.563, N.567, K.569 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.331, B:E.505, B:N.567 Water bridges: B:D.164 Salt bridges: B:R.563, B:K.569 SJ5.3: 11 residues within 4Å: Chain C: D.164, H.331, I.364, E.414, Y.469, Y.473, E.505, W.550, R.563, N.567, K.569 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.331, C:Y.473, C:E.505, C:N.567 Water bridges: C:D.164 Salt bridges: C:R.563, C:K.569 SJ5.4: 9 residues within 4Å: Chain D: D.164, H.331, E.414, Y.469, Y.473, E.505, W.550, N.567, K.569 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:D.164, D:H.331, D:N.467, D:Y.469, 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
C

D
D

Beta-D-glucuronidase

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