SMTL ID : 6a95.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.60 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: 6 residues within 4Å: Chain A: Q.329, N.373, T.385, C.386, L.387, 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: 1 residues within 4Å: Chain A: N.1058 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: W.341, N.355, H.358 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.355 NAG.5: 4 residues within 4Å: Chain A: N.351, S.354, N.355 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.354

1 x 9SR: (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name)(Non-covalent)

9SR.6: 13 residues within 4Å: Chain A: D.418, Y.419, E.421, E.744, E.747, F.1103, K.1104, G.1105, W.1106, L.1107, G.1397, D.1399 Ligands: NA.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.418, A:D.418, A:G.1105, A:W.1106, A:L.1107, A:G.1397 Salt bridges: A:E.744, A:E.747

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain A: D.418, E.744, W.745, I.746, E.747 Ligands: 9SR.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.418, A:W.745, A:I.746, 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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