SMTL ID : 5jlv.1 (1 other biounit)

Receptor binding domain of Botulinum neurotoxin A in complex with human glycosylated SV2C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 9 residues within 4Å: Chain A: F.85, H.196, Y.198, D.421, G.424 Chain B: I.88, D.89, K.108, N.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.421 Water bridges: A:E.425 Hydrophobic interactions: A:F.85, A:Y.198

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: D.141, R.145, N.164, N.365 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.164 Water bridges: A:W.146, A:N.164, A:N.164 Salt bridges: A:R.145

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 3 residues within 4Å: Chain A: K.160, L.167, Q.170 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.170, A:Q.170 Water bridges: A:N.158 Salt bridges: A:K.160 PO4.4: 4 residues within 4Å: Chain A: E.114, R.128, V.130, K.132 8 PLIP interactions: 8 interactions with chain A Water bridges: A:N.111, A:R.128, A:K.132, A:K.132, A:K.132, A:K.132 Salt bridges: A:R.128, A:K.132

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 2 residues within 4Å: Chain B: D.64, N.84 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yao, G. et al., N-linked glycosylation of SV2 is required for binding and uptake of botulinum neurotoxin A. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-06-15

Peptides

Botulinum neurotoxin type A: A
Synaptic vesicle glycoprotein 2C: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Botulinum neurotoxin type A

Synaptic vesicle glycoprotein 2C

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