SMTL ID : 7xmg.1

Cryo-EM structure of human NaV1.7/beta1/beta2-TCN-1752

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: 5 residues within 4Å: Chain A: N.1341, T.1343, D.1344, F.1348, S.1366 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: P.1354, N.1355, S.1357, E.1358, K.1412 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: M.1363, N.1364 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.1364 NAG.5: 3 residues within 4Å: Chain B: V.91, N.93, F.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.93 NAG.6: 2 residues within 4Å: Chain B: G.33, N.110 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain B: Q.61, N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.61 NAG.8: 2 residues within 4Å: Chain B: N.135, T.136 No protein-ligand interaction detected (PLIP)

1 x G4I: (1~{Z})-~{N}-[2-methyl-3-[(~{E})-[6-[4-[[4-(trifluoromethyloxy)phenyl]methoxy]piperidin-1-yl]-1~{H}-1,3,5-triazin-2-ylidene]amino]phenyl]ethanimidic acid(Non-covalent)

G4I.4: 13 residues within 4Å: Chain A: Q.360, F.391, I.394, N.395, L.398, L.953, L.1389, L.1438, N.1439, S.1686, I.1733, I.1734, F.1737 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.394, A:L.398, A:L.398, A:L.1438, A:L.1438, A:F.1737, A:F.1737, A:F.1737 Hydrogen bonds: A:Q.360, A:N.395

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Structural basis for Na V 1.7 inhibition by pore blockers. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-11-30

Peptides

Isoform 3 of Sodium channel protein type 9 subunit alpha,Green fluorescent protein: A
Sodium channel subunit beta-1,Green fluorescent protein: B
Sodium channel subunit beta-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

Membrane

We predict this structure to be a membrane protein.
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Isoform 3 of Sodium channel protein type 9 subunit alpha,Green fluorescent protein

Sodium channel subunit beta-1,Green fluorescent protein

Sodium channel subunit beta-2

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