SMTL ID : 6ed2.1

Faecalibacterium prausnitzii beta-glucuronidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: H.356, N.440, E.441, Y.497, E.535 Ligands: FMT.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.356, A:N.440, A:N.495, A:E.535 Water bridges: A:E.441 GOL.8: 6 residues within 4Å: Chain B: H.356, N.440, E.441, Y.497, E.535 Ligands: FMT.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.356, B:N.440, B:N.495, B:E.535 Water bridges: B:E.441 GOL.15: 6 residues within 4Å: Chain C: H.356, N.440, E.441, Y.497, E.535 Ligands: FMT.20 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.356, C:N.440, C:N.495, C:Y.497, C:E.535 GOL.22: 6 residues within 4Å: Chain D: H.356, N.440, E.441, Y.497, E.535 Ligands: FMT.27 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.356, D:N.440, D:N.495, D:Y.497, D:E.535

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.189, F.190, H.322, H.356, W.580, F.585 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: T.239, V.240, E.241, V.278, R.280 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.239, A:E.241 MG.9: 6 residues within 4Å: Chain B: D.189, F.190, H.322, H.356, W.580, F.585 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain B: T.239, V.240, E.241, V.278, R.280 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.239, B:E.241 MG.16: 6 residues within 4Å: Chain C: D.189, F.190, H.322, H.356, W.580, F.585 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain C: T.239, V.240, E.241, V.278, R.280 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.239, C:E.241 MG.23: 6 residues within 4Å: Chain D: D.189, F.190, H.322, H.356, W.580, F.585 No protein-ligand interaction detected (PLIP) MG.24: 5 residues within 4Å: Chain D: T.239, V.240, E.241, V.278, R.280 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.239, D:E.241

16 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 1 residues within 4Å: Chain C: N.558 Ligand excluded by PLIP FMT.5: 1 residues within 4Å: Chain A: R.216 Ligand excluded by PLIP FMT.6: 8 residues within 4Å: Chain A: D.189, Y.497, Y.501, W.580, R.593, N.597, K.599 Ligands: GOL.1 Ligand excluded by PLIP FMT.7: 6 residues within 4Å: Chain A: R.321, H.322, E.323, D.324, D.340, R.606 Ligand excluded by PLIP FMT.11: 1 residues within 4Å: Chain D: N.558 Ligand excluded by PLIP FMT.12: 1 residues within 4Å: Chain B: R.216 Ligand excluded by PLIP FMT.13: 8 residues within 4Å: Chain B: D.189, Y.497, Y.501, W.580, R.593, N.597, K.599 Ligands: GOL.8 Ligand excluded by PLIP FMT.14: 6 residues within 4Å: Chain B: R.321, H.322, E.323, D.324, D.340, R.606 Ligand excluded by PLIP FMT.18: 1 residues within 4Å: Chain A: N.558 Ligand excluded by PLIP FMT.19: 1 residues within 4Å: Chain C: R.216 Ligand excluded by PLIP FMT.20: 8 residues within 4Å: Chain C: D.189, Y.497, Y.501, W.580, R.593, N.597, K.599 Ligands: GOL.15 Ligand excluded by PLIP FMT.21: 6 residues within 4Å: Chain C: R.321, H.322, E.323, D.324, D.340, R.606 Ligand excluded by PLIP FMT.25: 1 residues within 4Å: Chain B: N.558 Ligand excluded by PLIP FMT.26: 1 residues within 4Å: Chain D: R.216 Ligand excluded by PLIP FMT.27: 8 residues within 4Å: Chain D: D.189, Y.497, Y.501, W.580, R.593, N.597, K.599 Ligands: GOL.22 Ligand excluded by PLIP FMT.28: 6 residues within 4Å: Chain D: R.321, H.322, E.323, D.324, D.340, R.606 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

Glycosyl hydrolase family 2, TIM barrel domain protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glycosyl hydrolase family 2, TIM barrel domain protein