SMTL ID : 6ec6.1

Ruminococcus gnavus Beta-glucuronidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 14 residues within 4Å: Chain A: D.190, H.358, N.391, F.392, N.440, E.441, Y.497, Y.501, E.535, W.580, F.585, R.593, N.597, K.599 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.190, A:H.358, A:N.440, A:Y.501, A:W.580, A:R.593, A:N.597, A:K.599 GOL.3: 14 residues within 4Å: Chain B: D.190, H.358, N.391, F.392, N.440, E.441, Y.497, Y.501, E.535, W.580, F.585, R.593, N.597, K.599 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.190, B:D.190, B:H.358, B:N.440, B:Y.501, B:W.580, B:R.593, B:N.597, B:K.599 GOL.5: 14 residues within 4Å: Chain C: D.190, H.358, N.391, F.392, N.440, E.441, Y.497, Y.501, E.535, W.580, F.585, R.593, N.597, K.599 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:D.190, C:D.190, C:H.358, C:E.535, C:W.580, C:R.593, C:N.597, C:K.599 Water bridges: C:D.190, C:D.190 GOL.7: 14 residues within 4Å: Chain D: D.190, H.358, N.391, F.392, N.440, E.441, Y.497, Y.501, E.535, W.580, F.585, R.593, N.597, K.599 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:D.190, D:H.358, D:E.535, D:W.580, D:R.593, D:N.597, D:K.599 Water bridges: D:D.190, D:D.190

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: D.84, H.85 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain B: D.84, H.85 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain C: D.84, H.85 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain D: D.84, H.85 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biernat, K.A. et al., Structure, function, and inhibition of drug reactivating human gut microbial beta-glucuronidases. Sci Rep (2019)

Release Date

2019-02-13

Peptides

Beta-glucuronidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Beta-glucuronidase