SMTL ID : 2bvl.1

Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.288, E.515 Ligands: UDP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.288, A:E.515, H2O.14, H2O.14

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

UDP.2: 18 residues within 4Å: Chain A: V.101, W.102, I.103, N.139, L.265, A.266, S.269, R.273, Y.284, D.286, V.287, D.288, E.515, S.518, L.519, W.520 Ligands: MN.1, GLC.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.265, A:L.519 Hydrogen bonds: A:V.101, A:I.103, A:I.103, A:N.139, A:S.269, A:Y.284, A:D.286, A:V.287, A:S.518, A:L.519 Water bridges: A:V.101, A:K.142, A:K.142, A:D.288, A:K.463, A:A.517 pi-Stacking: A:W.102

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

GLC.3: 12 residues within 4Å: Chain A: A.266, D.270, R.273, D.286, I.383, N.384, Q.385, T.465, G.470, P.471, W.520 Ligands: UDP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.273, A:R.273, A:D.286, A:Q.385 Water bridges: A:Q.385

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

SO4.4: 6 residues within 4Å: Chain A: M.516, A.517, S.518, F.522, D.523, R.526 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.516, A:S.518, A:D.523, A:D.523 Water bridges: A:R.526 Salt bridges: A:R.526

4 x TBR: HEXATANTALUM DODECABROMIDE(Non-covalent)

TBR.5: 4 residues within 4Å: Chain A: D.29, E.32, E.33, N.36 No protein-ligand interaction detected (PLIP) TBR.6: 7 residues within 4Å: Chain A: D.310, N.378, S.379, K.380, I.383, E.515, M.516 No protein-ligand interaction detected (PLIP) TBR.7: 7 residues within 4Å: Chain A: E.77, V.80, T.81, L.84, I.494, A.496, D.497 No protein-ligand interaction detected (PLIP) TBR.8: 6 residues within 4Å: Chain A: R.173, N.425, T.428, N.429, I.432, R.455 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reinert, D.J. et al., Structural Basis for the Function of Clostridium Difficile Toxin B. J.Mol.Biol. (2005)

Release Date

2005-08-03

Peptides

TOXIN B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

TOXIN B