SMTL ID : 6jz4.1

b-glucuronidase from Ruminococcus gnavus in complex with D-glucaro-d-lactam

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x EVA: (2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxopiperidine-2-carboxylic acid(Non-covalent)

EVA.1: 13 residues within 4Å: Chain A: D.191, H.359, N.441, E.442, N.496, Y.498, Y.502, E.536, W.581, F.586, R.594, N.598, K.600 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.191, A:H.359, A:N.441, A:E.442, A:N.496, A:Y.502, A:N.598 Water bridges: A:D.191, A:E.442, A:Y.502 Salt bridges: A:R.594, A:K.600 EVA.3: 13 residues within 4Å: Chain B: D.191, H.359, N.441, E.442, N.496, Y.498, Y.502, E.536, W.581, F.586, R.594, N.598, K.600 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.191, B:D.191, B:H.359, B:N.441, B:N.496, B:Y.498, B:Y.502, B:E.536, B:W.581, B:N.598 Salt bridges: B:R.594, B:K.600

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 9 residues within 4Å: Chain A: D.94, R.122, G.123, T.124, S.134, H.135, K.161, I.162, N.163 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.161 Water bridges: A:N.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dashnyam, P. et al., Substituent Position of Iminocyclitols Determines the Potency and Selectivity for Gut Microbial Xenobiotic-Reactivating Enzymes. J.Med.Chem. (2020)

Release Date

2020-06-03

Peptides

Beta-glucuronidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-glucuronidase

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