SMTL ID : 6a91.1

Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana bound with saxitoxin and Dc1a

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

hetero-1-1-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: 4 residues within 4Å: Chain A: Q.329, N.373, C.386, Q.388 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.1077 Chain B: Y.33 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: D.364, N.1058 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: W.341, N.355, H.358 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: N.351, S.354 No protein-ligand interaction detected (PLIP)

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.6: 7 residues within 4Å: Chain A: S.654, F.655, M.1042, N.1128, Y.1130, M.1131, F.1137 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.655 PC1.7: 9 residues within 4Å: Chain A: I.1033, H.1089, G.1091, N.1092, L.1095, R.1427, A.1428, I.1431, I.1439 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.1095, A:A.1428, A:I.1431, A:I.1439 Hydrogen bonds: A:N.1092 Salt bridges: A:H.1089, A:H.1089, A:R.1427, A:R.1427

1 x 9SL: [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate(Non-covalent)

9SL.8: 13 residues within 4Å: Chain A: Y.419, E.421, E.744, E.747, F.1103, K.1104, G.1105, W.1106, L.1107, Q.1108, A.1396, G.1397, D.1399 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.419, A:Y.419, A:E.421, A:E.744, A:G.1105, A:W.1106, A:L.1107, A:Q.1108, A:Q.1108, A:G.1397 Salt bridges: A:E.421, A:E.747

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, H. et al., Structural basis for the modulation of voltage-gated sodium channels by animal toxins. Science (2018)

Release Date

2018-08-08

Peptides

Sodium channel protein PaFPC1: A
Mu-diguetoxin-Dc1a: 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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Sodium channel protein PaFPC1

Mu-diguetoxin-Dc1a

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