SMTL ID : 7uib.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 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, N.62, C.63, T.64, R.84 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain B: N.67, N.87 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain D: A.7, N.8 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.7 NAG.7: 2 residues within 4Å: Chain D: T.10, N.12 1 PLIP interactions: 1 interactions with chain D Water bridges: D:T.10 NAG.8: 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)

SO4.4: 5 residues within 4Å: Chain B: F.76, Y.78 Chain E: K.326, T.378 Ligands: SO4.5 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 SO4.5: 7 residues within 4Å: Chain B: S.56, N.57, T.58, Y.78, K.79 Chain E: K.326 Ligands: SO4.4 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:N.57, B:T.58, B:Y.78 Salt bridges: B:K.79, E:K.326 SO4.10: 3 residues within 4Å: Chain D: N.57, 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: 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 SO4.13: 3 residues within 4Å: Chain E: K.239, E.240, K.283 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.238, E:E.240 Salt bridges: E:K.283 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 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.240 Salt bridges: F:K.239, F:K.283

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 6 residues within 4Å: Chain D: Y.71, H.92 Chain E: D.254, R.255, R.256, K.257 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:K.257, E:A.309, D:Y.71

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

SLB.11: 7 residues within 4Å: Chain E: Y.34, Y.36, G.44, Y.46, R.77, Y.196, E.401 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:Y.34, E:Y.36 Hydrogen bonds: E:Y.36, E:Y.46, E:Y.46, E:R.77, E:R.77, E:Y.196, E:Y.196, E:E.401 Water bridges: E:H.402 Salt bridges: E:H.402 SLB.14: 10 residues within 4Å: Chain F: Y.34, Y.36, G.44, Y.46, R.77, N.143, Y.196, E.401, H.402, G.403 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:Y.34, F:Y.36 Hydrogen bonds: F:Y.36, F:Y.36, F:Y.46, F:Y.46, F:R.77, F:R.77, F:Y.196, F:E.401, F:H.402, F:G.403

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
SV2: 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

SV2

Neurotoxin type E

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