SMTL ID : 9fyr.1

Cryo-EM structure of native SV2A in complex with TeNT-Hc, Pro-Macrobody 5 and Levetiracetam

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-FUC.1: 5 residues within 4Å: Chain A: E.533, N.553, V.555, N.573 Chain C: D.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.533

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

NAG-NAG.2: 2 residues within 4Å: Chain A: D.528, N.548 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.498 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.498

1 x 6UZ: omega-undecylenyl-beta-D-maltopyranoside(Non-covalent)

6UZ.4: 18 residues within 4Å: Chain A: E.490, V.492, V.495, F.497, F.499, L.501, H.506, Y.511, F.516, L.519, L.521, F.526, F.531, F.536, V.539, F.546 Chain B: T.312, Y.319 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.516, A:L.519, A:F.526, A:F.526, A:F.531, A:F.536, A:F.536 Hydrogen bonds: B:T.312, B:T.312, B:Y.319

1 x UKX: (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide(Non-covalent)

UKX.5: 14 residues within 4Å: Chain A: I.273, F.277, C.297, W.300, W.454, Y.461, Y.462, I.663, W.666, N.667, D.670, N.690, C.693, K.694 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.300, A:W.300, A:W.666 Hydrogen bonds: A:Y.462, A:N.667

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schenck, S. et al., Structures of native SV2A reveal the binding mode for tetanus neurotoxin and anti-epileptic racetams. Nat Commun (2025)

Release Date

2025-05-21

Peptides

Synaptic vesicle glycoprotein 2A: A
Tetanus toxin heavy chain: B
Pro-Macrobody 5,Maltose/maltodextrin-binding periplasmic protein,Maltose/maltodextrin-binding periplasmic protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

Membrane

We predict this structure to be a membrane protein.
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Synaptic vesicle glycoprotein 2A

Tetanus toxin heavy chain

Pro-Macrobody 5,Maltose/maltodextrin-binding periplasmic protein,Maltose/maltodextrin-binding periplasmic protein

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