SMTL ID : 8uo8.1

Structure of synaptic vesicle protein 2B with padsevonil

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: T.439, N.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.439, A:N.441 NAG.2: 1 residues within 4Å: Chain A: N.516 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.516 NAG.3: 2 residues within 4Å: Chain A: D.471, N.491 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.471

1 x X3U: (4R)-4-(2-chloro-2,2-difluoroethyl)-1-{[(4R)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}pyrrolidin-2-one(Non-covalent)

X3U.4: 17 residues within 4Å: Chain A: L.216, F.220, G.240, W.243, W.397, Y.404, Y.405, V.549, C.600, S.603, I.604, W.607, N.608, D.611, N.631, C.634, K.635 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.404, A:I.604, A:W.607, A:W.607 Hydrogen bonds: A:K.635 Halogen bonds: A:N.608

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

PS1.5: 6 residues within 4Å: Chain A: H.104, G.105, W.109, I.110, F.113, K.328 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.110

2 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.6: 5 residues within 4Å: Chain A: M.120, T.245, A.252, M.253, S.256 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.245 Hydrogen bonds: A:S.256 9Z9.7: 4 residues within 4Å: Chain A: K.231, E.234, I.554, L.558 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.554, A:L.558

1 x 43Y: [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate(Non-covalent)

43Y.8: 9 residues within 4Å: Chain A: M.253, S.256, I.257, Y.271, F.273, H.274, S.275, V.278, V.282 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.278, A:V.282

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.9: 13 residues within 4Å: Chain A: S.548, P.551, G.552, I.555, I.563, K.567, M.568, G.571, I.575, C.597, L.598, G.601, T.602 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.551, A:I.555, A:I.563, A:I.575 Hydrogen bonds: A:G.552

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 2B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Synaptic vesicle glycoprotein 2B