SMTL ID : 3obt.1

Crystal structure of Botulinum neurotoxin serotype D ligand binding domain in complex with N-Acetylneuraminic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x SLB: N-acetyl-beta-neuraminic acid(Non-covalent)

SLB.1: 6 residues within 4Å: Chain A: S.260, D.316, T.317, D.318, K.337, R.384 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.317, A:D.318, A:D.318, A:K.337, A:R.384, A:R.384 Water bridges: A:R.384 Salt bridges: A:K.337, A:R.384

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: N.331, C.332, V.333, V.396, T.397, N.398, K.402 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.331, A:C.332, A:T.397 GOL.3: 6 residues within 4Å: Chain A: N.99, S.100, I.101, D.183, T.185, V.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.99, A:I.101, A:D.183 GOL.4: 7 residues within 4Å: Chain A: R.254, E.259, V.264, L.265, V.266, A.390, Y.391 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.254, A:E.259, A:Y.391 GOL.5: 5 residues within 4Å: Chain A: E.94, K.108, I.119, Q.121, Y.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.94, A:K.108, A:Q.121, A:Q.121 GOL.6: 4 residues within 4Å: Chain A: S.260, W.383, S.386, K.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.260, A:S.386, A:K.388 GOL.7: 5 residues within 4Å: Chain A: K.273, Y.275, R.415, E.421, P.422 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.415, A:R.415 GOL.8: 3 residues within 4Å: Chain A: Y.255, P.269, T.276 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.277, A:N.278, A:N.278 GOL.9: 6 residues within 4Å: Chain A: N.278, P.279, L.305, Y.306, N.307, S.308 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.278, A:N.307, A:N.307, A:S.308, A:S.308 GOL.10: 7 residues within 4Å: Chain A: N.113, N.115, D.133, S.135, E.136, S.137, L.138 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.115, A:D.133, A:S.135, A:E.136, A:S.137 Water bridges: A:N.113 GOL.11: 7 residues within 4Å: Chain A: M.6, N.10, K.13, Q.18, N.206, V.220, Q.224 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.13, A:Q.18, A:N.206, A:Q.224 Water bridges: A:S.16, A:N.206 GOL.12: 5 residues within 4Å: Chain A: N.43, T.44, I.45, T.47, R.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.43, A:T.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strotmeier, J. et al., Botulinum neurotoxin serotype D attacks neurons via two carbohydrate-binding sites in a ganglioside-dependent manner. Biochem.J. (2010)

Release Date

2010-09-08

Peptides

Botulinum neurotoxin type D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Botulinum neurotoxin type D

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