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

Structure of the GTD domain of Clostridium difficile toxin A in complex with VHH AH3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

UPG.1: 25 residues within 4Å: Chain A: V.101, W.102, I.103, N.139, L.265, A.266, S.269, D.270, R.273, Y.284, D.286, V.287, D.288, I.383, N.384, Q.385, T.465, I.466, G.470, P.471, E.515, S.518, L.519, W.520 Ligands: MN.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.265 Hydrogen bonds: A:V.101, A:I.103, A:I.103, A:N.139, A:S.269, A:R.273, A:R.273, A:Y.284, A:V.287, A:N.384, A:Q.385, A:L.519 Water bridges: A:V.101, A:D.286, A:D.288 pi-Stacking: A:W.102

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

MN.2: 3 residues within 4Å: Chain A: D.288, E.515 Ligands: UPG.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.288, A:E.515, H2O.1

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: N.405, F.409, Q.412, I.489 Ligands: PEG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.412 PEG.4: 5 residues within 4Å: Chain A: F.409, T.440, E.442, N.443 Ligands: PEG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.440, A:N.443

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

EDO.5: 3 residues within 4Å: Chain A: K.174, E.177, T.425 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.174 Water bridges: A:T.425 EDO.6: 5 residues within 4Å: Chain A: Y.180, D.181, K.184, N.422, N.423 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.184 EDO.7: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.538 EDO.8: 3 residues within 4Å: Chain A: P.93, N.365, N.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.365, A:N.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, B. et al., Neutralizing epitopes on Clostridioides difficile toxin A revealed by the structures of two camelid VHH antibodies. Front Immunol (2022)

Release Date

2022-11-16

Peptides

Glucosyltransferase TcdA: A
Nanobody VHH AH3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Glucosyltransferase TcdA

Nanobody VHH AH3

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