SMTL ID : 6thy.1

Botulinum neurotoxin A3 Hc domain in complex with GD1a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x BGC- GAL- NGA- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-functional Binders)

BGC-GAL-NGA-GAL-SIA.1: 10 residues within 4Å: Chain A: F.254, V.339, E.340, F.389, H.390, S.401, W.403, Y.404, F.415, G.416 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.340, A:S.401, A:S.401, A:H.390, A:F.389, A:G.416 Water bridges: A:H.390, A:L.391 Hydrophobic interactions: A:F.254, A:F.389

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.2: 8 residues within 4Å: Chain A: Y.42, Y.43, D.44, K.52, I.54, Y.203, M.205, D.426 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.43, A:K.52 Water bridges: A:S.45

2 x EDO: 1,2-ETHANEDIOL(Non-covalent)

EDO.3: 4 residues within 4Å: Chain A: N.67, V.70, H.185, N.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.188 Water bridges: A:N.188 EDO.5: 3 residues within 4Å: Chain A: N.55, C.197, R.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.55

1 x ACT: ACETATE ION(Non-covalent)

ACT.4: 5 residues within 4Å: Chain A: I.69, Y.71, F.78, W.111, L.211 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.71 Water bridges: A:Y.71

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

PEG.6: 8 residues within 4Å: Chain A: K.137, Y.138, S.139, V.142, I.144, S.145, D.146, Y.147 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.137, A:S.139, A:I.144, A:D.146 PEG.7: 7 residues within 4Å: Chain A: M.141, V.142, N.143, S.279, L.287, N.288, S.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.279 Water bridges: A:M.141

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Gregory, K.S. et al., Crystal structure of botulinum neurotoxin subtype A3 cell binding domain in complex with GD1a co-receptor ganglioside. Febs Open Bio (2020)

Release Date

2020-01-29

Peptides

BoNT/A3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

BoNT/A3

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