SMTL ID : 6oq7.1

Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH E3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-1-1-mer

Ligands

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

UDP.1: 19 residues within 4Å: Chain A: I.101, W.102, I.103, N.139, L.265, A.266, S.269, Y.284, D.286, V.287, D.288, E.516, N.518, S.519, L.520, W.521 Ligands: GLC.2, MN.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.265 Hydrogen bonds: A:I.101, A:I.103, A:I.103, A:N.139, A:S.269, A:Y.284, A:V.287, A:L.520, A:W.521 Water bridges: A:I.101, A:D.286, A:D.288 pi-Stacking: A:W.102

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.2: 13 residues within 4Å: Chain A: A.266, D.270, R.273, D.286, I.384, N.385, Q.386, T.466, I.467, G.471, P.472, W.521 Ligands: UDP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.273, A:R.273, A:D.286, A:Q.386, A:T.466

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

MN.3: 4 residues within 4Å: Chain A: D.288, E.516 Ligands: UDP.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.288, A:E.516, H2O.1, H2O.2

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.288, Q.515, N.518 Ligands: UDP.1, MN.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.288, A:Q.515, A:N.518, H2O.2, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, P. et al., Structure of the full-length Clostridium difficile toxin B. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-07-10

Peptides

Toxin B: A
E3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Toxin B

E3

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