SMTL ID : 7uia.1

Crystal structure of BoNT/E receptor binding domain in complex with SV2 and VHH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain B: A.7, N.8 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain B: R.3, D.42, S.43, V.44, N.62, C.63, T.64 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain B: N.12 Chain F: S.335 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F Water bridges: B:N.12, B:N.12 Hydrogen bonds: F:S.335 NAG.4: 2 residues within 4Å: Chain B: N.67, N.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.67, B:N.87 NAG.7: 2 residues within 4Å: Chain D: A.7, N.8 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.7 NAG.8: 1 residues within 4Å: Chain D: N.12 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.12 NAG.9: 5 residues within 4Å: Chain D: D.42, S.43, N.62, C.63, T.64 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.42 NAG.10: 2 residues within 4Å: Chain D: N.67, N.87 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.67, D:N.87

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

SO4.5: 5 residues within 4Å: Chain B: F.76, Y.78 Chain E: K.326, T.378, W.379 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:T.378 Salt bridges: E:K.326 Water bridges: B:D.74 SO4.6: 4 residues within 4Å: Chain B: S.56, N.57, Y.78 Chain E: K.326 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain B Salt bridges: E:K.326, B:K.79 Hydrogen bonds: B:N.57, B:T.58, B:Y.78 Water bridges: B:K.79 SO4.11: 5 residues within 4Å: Chain D: S.56, N.57, F.59, Y.78, K.79 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.57, D:Y.78 Salt bridges: D:K.79 SO4.12: 2 residues within 4Å: Chain E: K.239, E.240 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.240 Salt bridges: E:K.283 SO4.13: 3 residues within 4Å: Chain E: N.223, N.225, R.298 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.223 Salt bridges: E:R.298 SO4.15: 3 residues within 4Å: Chain F: N.223, N.225, R.298 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.223, F:N.225 Salt bridges: F:R.298 SO4.16: 2 residues within 4Å: Chain F: K.239, E.240 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.240 Water bridges: F:K.283, F:K.283 Salt bridges: F:K.239, F:K.283

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

PEG.14: 5 residues within 4Å: Chain F: N.96, M.98, R.99, S.181, D.182 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.181, F:D.182, F:D.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Z. et al., Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2. Nat Commun (2023)

Release Date

2023-04-05

Peptides

VHH-G6: AC
SV2Ac: BD
Neurotoxin type E: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
E

B
C

D
F

E
D

F
A

VHH-G6

SV2Ac

Neurotoxin type E

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