SMTL ID : 8y2l.1

The Crystal Structure of Glucosyltransferase TcdB from Clostridioides difficile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.95 Å

Oligo State

homo-trimer

Ligands

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.291, E.518, S.521 Ligands: UDP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.291, A:E.518, A:S.521, H2O.1 MN.3: 4 residues within 4Å: Chain B: D.291, E.518, S.521 Ligands: UDP.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.291, B:E.518, B:S.521, H2O.1 MN.5: 4 residues within 4Å: Chain C: D.291, E.518, S.521 Ligands: UDP.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.291, C:E.518, C:S.521, H2O.1

3 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 13 residues within 4Å: Chain A: V.104, W.105, I.106, L.268, S.272, R.276, Y.287, D.289, V.290, D.291, E.518, S.521 Ligands: MN.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:V.104, A:I.106, A:I.106, A:S.272, A:R.276, A:Y.287, A:V.290 Water bridges: A:D.289, A:D.289 pi-Stacking: A:W.105 UDP.4: 15 residues within 4Å: Chain B: V.104, W.105, I.106, N.142, L.268, A.269, S.272, R.276, Y.287, D.289, V.290, D.291, E.518, S.521 Ligands: MN.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:V.104, B:I.106, B:I.106, B:S.272, B:R.276, B:Y.287, B:V.290 pi-Stacking: B:W.105 UDP.6: 13 residues within 4Å: Chain C: V.104, W.105, I.106, L.268, S.272, R.276, Y.287, D.289, V.290, D.291, E.518, S.521 Ligands: MN.5 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:V.104, C:I.106, C:I.106, C:S.272, C:R.276, C:Y.287, C:V.290 Water bridges: C:D.289, C:D.289 pi-Stacking: C:W.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, S. et al., The Crystal Structure of Glucosyltransferase TcdB from Clostridioides difficile. To Be Published

Release Date

2025-01-29

Peptides

Glucosyltransferase TcdB: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Glucosyltransferase TcdB