SMTL ID : 6j8i.1

Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (Y1755 up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-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 B: N.1395, T.1397, D.1398, S.1420 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: P.1408, N.1409, S.1411, E.1412 No protein-ligand interaction detected (PLIP)

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

NAG.3: 5 residues within 4Å: Chain A: S.64, N.66, M.79, Q.82, R.137 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.82 Hydrogen bonds: A:S.64, A:R.137 NAG.4: 1 residues within 4Å: Chain B: N.1418 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain B: N.325, N.326 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.325 NAG.7: 4 residues within 4Å: Chain C: V.91, W.92, N.93, R.96 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.96 NAG.8: 1 residues within 4Å: Chain C: N.110 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain C: Q.61, N.114 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.61, C:Q.61 NAG.10: 2 residues within 4Å: Chain C: Y.124, N.135 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.124

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: 12 residues within 4Å: Chain B: D.404, Y.405, E.407, E.970, E.973, F.1448, K.1449, G.1450, W.1451, T.1452, G.1742, D.1744 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:D.404, B:Y.405, B:Y.405, B:Y.405, B:E.407, B:R.965, B:F.1448, B:G.1450, B:T.1452, B:T.1452, B:T.1452, B:G.1742, B:D.1744 Salt bridges: B:E.407, B:E.970, B:E.973

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, H. et al., Structures of human Nav1.7 channel in complex with auxiliary subunits and animal toxins. Science (2019)

Release Date

2019-02-27

Peptides

Sodium channel subunit beta-2: A
Sodium channel protein type 9 subunit alpha: B
Sodium channel subunit beta-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Membrane

We predict this structure to be a membrane protein.
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Sodium channel subunit beta-2

Sodium channel protein type 9 subunit alpha

Sodium channel subunit beta-1

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