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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x NOY: (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL(Non-covalent)

NOY.1: 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.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.521 Hydrogen bonds: A:R.274, A:R.274, A:D.287, A:D.287, A:Q.386, A:T.466 Water bridges: A:D.287

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

UDP.2: 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: NOY.1, MN.6 17 PLIP interactions: 17 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:A.518, A:S.519, A:L.520 Water bridges: A:V.102, A:D.287, A:D.287, A:D.289 pi-Stacking: A:W.103

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: E.246, F.247, G.250, S.252, S.276, K.279, E.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.251, A:S.252, A:S.276, A:K.279 GOL.4: 5 residues within 4Å: Chain A: V.81, L.483, H.493, L.494, D.498 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.483, A:H.493, A:D.498 GOL.5: 4 residues within 4Å: Chain A: W.103, N.109, A.112, Q.515 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.109, A:Q.515 Water bridges: A:V.288

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

MN.6: 3 residues within 4Å: Chain A: D.289, E.516 Ligands: UDP.2 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

Toxin B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Toxin B

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