SMTL ID : 5uj6.1

Crystal Structure of Bacteroides Uniformis beta-glucuronidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: D.158, H.355, N.417, E.418, N.485, Y.487, E.518, W.565, F.570, N.583 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.158, A:H.355, A:N.417, A:N.485, A:E.518, A:E.518, A:W.565 Water bridges: A:D.158, A:Y.487, A:N.583 GOL.2: 5 residues within 4Å: Chain A: T.620, N.674, R.693, I.694, N.695 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.674, A:N.695 Water bridges: A:T.620, A:T.620 GOL.3: 11 residues within 4Å: Chain A: E.727, N.759, T.760, A.761, D.762, F.766, R.844 Chain B: I.327, A.330, T.332, M.335 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.760, A:A.761, A:D.762, A:D.762 Water bridges: A:R.844 GOL.6: 9 residues within 4Å: Chain A: T.332, M.335 Chain B: E.727, N.759, T.760, A.761, D.762, F.766, R.844 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.727, B:A.761, B:D.762, B:D.762, B:R.844 Water bridges: B:E.727, B:N.759, B:R.844 GOL.7: 11 residues within 4Å: Chain B: D.158, H.321, H.355, N.417, E.418, N.485, Y.487, E.518, W.565, F.570, N.583 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.417, B:E.418, B:N.485, B:W.565 Water bridges: B:D.158, B:D.158, B:H.355, B:N.583 GOL.8: 5 residues within 4Å: Chain B: T.620, N.674, R.693, I.694, N.695 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.620, B:N.674, B:N.695 Water bridges: B:T.620, B:D.621, B:N.674, B:N.695

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.168, D.333, D.359, A.361 Chain B: K.846 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.168, A:D.359, H2O.4, H2O.6, H2O.23 CA.9: 5 residues within 4Å: Chain A: K.846 Chain B: D.168, D.333, D.359, A.361 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.168, B:D.333, B:D.333, B:D.359, H2O.41

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

NA.5: 6 residues within 4Å: Chain A: N.716, V.717, L.765, T.768, L.769, N.870 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.717, A:T.768 NA.10: 6 residues within 4Å: Chain B: N.716, V.717, L.765, T.768, L.769, N.870 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.870

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pollet, R.M. et al., An Atlas of beta-Glucuronidases in the Human Intestinal Microbiome. Structure (2017)

Release Date

2017-06-28

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

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