SMTL ID : 7xmf.1

Cryo-EM structure of human NaV1.7/beta1/beta2-Nav1.7-IN2

Coordinates

PDB Format

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: 6 residues within 4Å: Chain A: N.1341, T.1343, D.1344, F.1348, S.1366, V.1369 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)

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

NAG.3: 1 residues within 4Å: Chain A: N.1364 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.282, N.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.283 NAG.6: 4 residues within 4Å: Chain B: V.91, W.92, N.93, F.107 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain B: G.33, N.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.33, B:N.110 NAG.8: 3 residues within 4Å: Chain B: Q.61, E.84, N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.61 NAG.9: 3 residues within 4Å: Chain B: N.135, T.136, S.137 No protein-ligand interaction detected (PLIP)

1 x G2W: 3-[[4-[3-(4-fluoranyl-2-methyl-phenoxy)azetidin-1-yl]pyrimidin-2-yl]amino]-~{N}-methyl-benzamide(Non-covalent)

G2W.5: 9 residues within 4Å: Chain A: T.359, I.394, G.915, T.1393, L.1438, S.1686, I.1733, F.1737, V.1740 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.394, A:L.1438, A:F.1737 Hydrogen bonds: A:S.1686 pi-Stacking: A:F.1737

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
C

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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