SMTL ID : 6nzg.1

Bacteroides uniformis beta-glucuronidase 2 covalently bound to cyclophellitol-6-carboxylate aziridine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

2 x L9D: (1S,2R,3S,4S,5S,6R)-2-amino-3,4,5,6-tetrahydroxycyclohexane-1-carboxylic acid(Covalent)

L9D.1: 12 residues within 4Å: Chain A: D.158, H.355, N.417, E.418, N.485, Y.487, Y.491, E.518, W.565, F.570, N.583, K.585 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.518 Hydrogen bonds: A:D.158, A:D.158, A:N.417, A:E.418, A:E.418, A:N.583 Water bridges: A:H.355 Salt bridges: A:R.575, A:K.585 L9D.5: 14 residues within 4Å: Chain B: D.158, H.355, N.417, E.418, N.485, Y.487, Y.491, E.518, W.565, F.570, R.575, N.583, K.585 Ligands: GOL.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.487, B:E.518 Hydrogen bonds: B:D.158, B:N.417, B:E.418, B:E.418, B:Y.491, B:N.583 Water bridges: B:D.158, B:D.158, B:H.355, B:E.418 Salt bridges: B:R.575, B:K.585

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: E.727, T.760, A.761, D.762, F.766, R.844 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.760, A:A.761, A:D.762, A:D.762, A:R.844 Water bridges: A:R.844 GOL.6: 8 residues within 4Å: Chain A: T.332 Chain B: E.727, T.760, A.761, D.762, F.766, R.844 Ligands: GOL.8 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.727, B:A.761, B:D.762, B:R.844 Water bridges: A:A.330 GOL.7: 5 residues within 4Å: Chain B: E.418, L.421, R.425, Y.491 Ligands: L9D.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.418, B:R.425 GOL.8: 8 residues within 4Å: Chain A: T.332, E.334 Chain B: W.732, D.762, L.765, E.788, R.844 Ligands: GOL.6 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.762, B:D.762, A:E.334 Water bridges: B:R.844, B:R.844, A:D.333, A:E.334

2 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: N.716, V.717, L.765, T.768, N.870 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.717, A:L.765, A:T.768, A:T.768, A:N.870 K.9: 5 residues within 4Å: Chain B: N.716, V.717, L.765, T.768, N.870 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:V.717, B:L.765, B:T.768, B:T.768, B:N.870

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: D.168, D.333, D.359 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.168, A:D.359, H2O.2, H2O.5, H2O.9 CA.10: 3 residues within 4Å: Chain B: D.168, D.333, D.359 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.168, B:D.359, H2O.14, H2O.15, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jariwala, P.B. et al., Discovering the Microbial Enzymes Driving Drug Toxicity with Activity-Based Protein Profiling. Acs Chem.Biol. (2020)

Release Date

2019-12-18

Peptides

Beta-galactosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-galactosidase

Related Entries With Identical Sequence