SMTL ID : 5z19.2 (1 other biounit)

The crystal structure of Ruminococcus gnavus beta-glucuronidase in complex with uronic isofagomine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

SJ5.1: 13 residues within 4Å: Chain A: D.191, H.359, F.393, N.441, E.442, Y.498, Y.502, E.536, W.581, F.586, R.594, N.598, K.600 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.191, A:D.191, A:H.359, A:E.536, A:N.598 Salt bridges: A:R.594, A:K.600 SJ5.2: 13 residues within 4Å: Chain B: D.191, H.359, F.393, N.441, E.442, Y.498, Y.502, E.536, W.581, F.586, R.594, N.598, K.600 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.191, B:H.359, B:Y.502, B:E.536, B:W.581, B:N.598 Salt bridges: B:R.594, B:K.600 SJ5.3: 13 residues within 4Å: Chain C: D.191, H.359, F.393, N.441, E.442, Y.498, Y.502, E.536, W.581, F.586, R.594, N.598, K.600 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.191, C:H.359, C:Y.502, C:E.536, C:W.581, C:N.598 Salt bridges: C:R.594, C:K.600 SJ5.4: 12 residues within 4Å: Chain D: D.191, H.359, F.393, E.442, Y.498, Y.502, E.536, W.581, F.586, R.594, N.598, K.600 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:D.191, D:D.191, D:H.359, D:Y.498, D:E.536, D:N.598 Salt bridges: D:R.594, D:K.600

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dashnyam, P. et al., Dissection of the substrate preference and structure of gut microbial beta-glucuronidases identifies the major bacteria causing xenobiotic toxicity. To Be Published

Release Date

2018-12-12

Peptides

Beta-glucuronidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
B

Beta-glucuronidase

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