SMTL ID : 5uqm.1

Clostridium difficile Toxin B (TcdB) glucosyltransferase domain in complex with U2F

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.308, Q.405, E.535 Ligands: U2F.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.308, A:E.535, H2O.1, H2O.4

1 x U2F: URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE(Non-covalent)

U2F.2: 26 residues within 4Å: Chain A: V.121, W.122, I.123, N.159, L.285, A.286, S.289, D.290, R.293, Y.304, D.306, V.307, D.308, I.403, N.404, Q.405, T.485, I.486, S.489, G.490, P.491, E.535, S.538, L.539, W.540 Ligands: MN.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.285, A:L.539 Hydrogen bonds: A:V.121, A:I.123, A:I.123, A:N.159, A:S.289, A:D.290, A:D.290, A:R.293, A:R.293, A:Y.304, A:D.306, A:V.307, A:N.404, A:L.539, A:W.540 Water bridges: A:V.121, A:D.308, A:Q.405, A:Q.405 pi-Stacking: A:W.122 Halogen bonds: A:Q.405

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: M.536, A.537, S.538, S.541, F.542, D.543, R.546 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.536, A:S.538, A:D.543 Salt bridges: A:R.546 SO4.4: 2 residues within 4Å: Chain A: R.546, Q.550 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.550 Salt bridges: A:R.546

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alvin, J.W. et al., Clostridium difficile toxin glucosyltransferase domains in complex with a non-hydrolyzable UDP-glucose analogue. J. Struct. Biol. (2017)

Release Date

2017-05-10

Peptides

Toxin B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Toxin B

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