SMTL ID : 4isq.1 (2 other biounits)

Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: D.397, Y.398, W.399, F.400, H.402 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.397, A:D.397, A:Y.398, A:W.399, A:F.400 Salt bridges: A:H.402 SO4.2: 3 residues within 4Å: Chain A: R.331, S.391, N.401 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.391, A:S.391, A:N.401 Water bridges: A:N.401 Salt bridges: A:R.331 SO4.3: 5 residues within 4Å: Chain A: S.386, I.387, G.388, Y.390, L.417 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.386, A:Y.390, A:Y.390, A:S.422 SO4.4: 5 residues within 4Å: Chain A: E.349, K.352, Y.353 Chain B: K.10, K.14 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.10, B:K.14, A:K.352 Hydrogen bonds: A:Y.353 SO4.5: 2 residues within 4Å: Chain A: T.363, F.364 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.364 SO4.6: 2 residues within 4Å: Chain A: E.287, G.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.288

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: K.142, K.149, Y.244, V.260, M.263, D.365, Y.366 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.149, A:Y.244, A:V.260 GOL.8: 3 residues within 4Å: Chain A: S.389, E.403, L.405 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.389 Water bridges: A:E.403 GOL.9: 9 residues within 4Å: Chain A: F.48, P.49, W.86, W.150, R.214, Q.236, K.242, G.246, Y.367 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.214, A:Q.236, A:Y.367, A:Y.367 GOL.10: 4 residues within 4Å: Chain A: H.413, Y.414, A.415, S.416 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.415, A:S.416, A:S.416 Water bridges: A:K.410

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berntsson, R.P. et al., Crystal Structures of Botulinum Neurotoxin DC in Complex with Its Protein Receptors Synaptotagmin I and II. Structure (2013)

Release Date

2013-08-14

Peptides

Neurotoxin: A
Synaptotagmin-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

Neurotoxin

Synaptotagmin-1

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