SMTL ID : 7lou.1 (1 other biounit)

Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and isofagomine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: E.22, D.23, Y.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.23, A:D.23 EDO.2: 5 residues within 4Å: Chain A: Y.395, N.398, L.399, K.402, E.487 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.487 EDO.3: 7 residues within 4Å: Chain A: E.246, F.247, G.250, S.276, K.279, E.280, V.401 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: D.52, S.55, L.56, I.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.52 EDO.5: 4 residues within 4Å: Chain A: Y.324, K.325, L.351, A.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.325 EDO.6: 5 residues within 4Å: Chain A: N.54, D.58, K.77, M.484, K.486 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.77 EDO.7: 3 residues within 4Å: Chain A: D.311, N.379, S.380 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.380 Water bridges: A:N.379, A:K.506 EDO.8: 5 residues within 4Å: Chain A: K.183, N.186, Y.210, E.214, Y.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.183, A:N.186 EDO.9: 2 residues within 4Å: Chain A: M.38, K.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.49 Water bridges: A:E.34

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

UDP.10: 18 residues within 4Å: Chain A: V.102, W.103, I.104, N.140, L.266, A.267, S.270, R.274, Y.285, D.287, V.288, D.289, E.516, S.519, L.520, W.521 Ligands: IFM.11, MN.12 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.266, A:L.520 Hydrogen bonds: A:V.102, A:I.104, A:I.104, A:N.140, A:S.270, A:Y.285, A:V.288, A:S.519, A:L.520 Water bridges: A:V.102, A:D.287, A:D.289, A:Q.386, A:Q.386, A:A.518 pi-Stacking: A:W.103

1 x IFM: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE(Non-covalent)

IFM.11: 13 residues within 4Å: Chain A: A.267, D.271, R.274, D.287, I.384, N.385, Q.386, T.466, I.467, G.471, P.472, W.521 Ligands: UDP.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.274, A:R.274, A:D.287, A:T.466 Water bridges: A:W.521

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

MN.12: 3 residues within 4Å: Chain A: D.289, E.516 Ligands: UDP.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.289, A:E.516, H2O.1, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paparella, A.S. et al., Inhibition of Clostridium difficile TcdA and TcdB toxins with transition state analogues. Nat Commun (2021)

Release Date

2021-11-17

Peptides

Glucosyltransferase TcdB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucosyltransferase TcdB

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