SMTL ID : 6d1p.1

Apo structure of Bacteroides uniformis beta-glucuronidase 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

5 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: D.333, K.579, D.580, F.581 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.333, A:D.580 Water bridges: A:H.331 NA.2: 5 residues within 4Å: Chain A: T.174, D.434, F.435 Chain B: S.44, W.46 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.44, A:D.434 Water bridges: B:I.45 NA.10: 4 residues within 4Å: Chain A: S.44 Chain B: T.174, D.434, F.435 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.44, B:T.174, B:T.174 Water bridges: A:I.45 NA.11: 4 residues within 4Å: Chain B: D.333, K.579, D.580, F.581 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.333, B:D.333 NA.12: 3 residues within 4Å: Chain B: E.175, S.398, Y.399 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.398

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: I.209, E.210, A.211, F.303, G.304, N.416, P.418, T.460, R.461 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.211, A:G.304, A:T.460, A:T.460, A:R.461 Water bridges: A:R.306, A:R.461 GOL.4: 9 residues within 4Å: Chain A: D.183, H.365, R.391, N.427, E.428, R.466, E.512, W.576 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.427, A:N.427, A:W.576 Water bridges: A:D.183, A:H.365 GOL.5: 8 residues within 4Å: Chain A: R.391, E.428, R.466, W.483, Y.487, E.512 Ligands: GOL.4, SCN.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.391, A:R.466, A:R.466, A:E.512 Water bridges: A:D.183, A:R.391 GOL.13: 8 residues within 4Å: Chain B: D.183, H.365, N.427, E.428, R.466, E.512, W.576 Ligands: GOL.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.391, B:N.427, B:N.427, B:R.466, B:W.576 Water bridges: B:D.183, B:D.183 GOL.14: 8 residues within 4Å: Chain B: R.391, E.428, W.431, R.466, W.483, Y.487, E.512 Ligands: GOL.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.391, B:E.428, B:R.466, B:R.466, B:W.483, B:Y.487 Water bridges: B:D.183, B:K.597

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.6: 3 residues within 4Å: Chain A: R.467, T.481 Ligands: GOL.5 No protein-ligand interaction detected (PLIP) SCN.7: 4 residues within 4Å: Chain A: T.481, W.483, G.488, M.497 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.8: 5 residues within 4Å: Chain A: D.77, A.78, D.80, V.83, Y.593 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.77, A:A.78, A:D.80, A:V.83, H2O.6 K.9: 6 residues within 4Å: Chain A: D.173, M.176, P.178, S.179, D.180, L.186 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.173, A:M.176, A:P.178, H2O.1 K.15: 5 residues within 4Å: Chain B: D.77, A.78, D.80, V.83, Y.593 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.77, B:A.78, B:D.80, B:V.83, H2O.27 K.16: 5 residues within 4Å: Chain B: D.173, M.176, P.178, S.179, D.180 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.173, B:M.176, B:P.178, H2O.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pellock, S.J. et al., Three structurally and functionally distinct beta-glucuronidases from the human gut microbeBacteroides uniformis. J. Biol. Chem. (2018)

Release Date

2018-10-17

Peptides

Glycosyl hydrolases family 2, sugar binding domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycosyl hydrolases family 2, sugar binding domain protein