SMTL ID : 8uo9.1

Structure of synaptic vesicle protein 2A in complex with a nanobody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 1 residues within 4Å: Chain A: N.511 No protein-ligand interaction detected (PLIP)

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.2: 1 residues within 4Å: Chain A: N.486 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.436 No protein-ligand interaction detected (PLIP)

1 x X49: (4S)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}-4-(4,4,4-trifluorobutyl)pyrrolidin-2-one(Non-covalent)

X49.4: 18 residues within 4Å: Chain A: I.211, F.215, C.235, W.238, M.239, W.392, Y.399, Y.400, V.546, G.597, S.600, I.601, W.604, N.605, D.608, F.624, N.628, C.631 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.238, A:I.601, A:W.604 pi-Stacking: A:W.604, A:W.604 Halogen bonds: A:G.597

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.5: 12 residues within 4Å: Chain A: P.548, G.549, V.552, K.559, I.560, R.564, M.565, G.568, S.569, M.572, G.598, V.599 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.548, A:V.552, A:V.552, A:I.560, A:I.560, A:R.564, A:V.599 Salt bridges: A:K.559, A:R.564, A:R.564

1 x PS1: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE](Non-covalent)

PS1.6: 6 residues within 4Å: Chain A: V.571, A.662, S.665, S.666, L.669, K.670 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.571 Salt bridges: A:K.670

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mittal, A. et al., Structures of synaptic vesicle protein 2A and 2B bound to anticonvulsants. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-05-22

Peptides

Synaptic vesicle glycoprotein 2A: A
Nanobody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

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

Nanobody

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