SMTL ID : 6jz1.1

Apo structure of b-glucuronidase from Ruminococcus gnavus at 1.7 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-tetramer

Ligands

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

MRD.1: 8 residues within 4Å: Chain A: R.98, G.99, T.100, S.110, H.111, K.137, I.138, N.139 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.137, A:N.139 Water bridges: A:N.139 MRD.2: 5 residues within 4Å: Chain B: E.144, G.361, M.362, R.364, L.389 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.364 MRD.3: 7 residues within 4Å: Chain B: R.98, G.99, T.100, S.110, H.111, K.137, N.139 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.137, B:N.139 Water bridges: B:K.137, B:N.139 MRD.4: 8 residues within 4Å: Chain C: R.98, G.99, T.100, S.110, H.111, K.137, I.138, N.139 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.137, C:N.139 Water bridges: C:N.139 MRD.5: 5 residues within 4Å: Chain D: E.144, G.361, M.362, R.364, L.389 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:R.364 Hydrogen bonds: D:E.382 MRD.6: 7 residues within 4Å: Chain D: R.98, G.99, T.100, S.110, H.111, K.137, N.139 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:K.137, D:N.139 Water bridges: D:K.137, D:N.139

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Beta-glucuronidase

Related Entries With Identical Sequence