SMTL ID : 7xm9.1

Cryo-EM structure of human NaV1.7/beta1/beta2-XEN907

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: 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: 4 residues within 4Å: Chain A: P.1354, N.1355, S.1357, E.1358 No protein-ligand interaction detected (PLIP)

5 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.6: 5 residues within 4Å: Chain B: K.37, W.92, N.93, F.107, T.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.93 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.61, B:N.114 NAG.9: 2 residues within 4Å: Chain B: N.135, T.136 No protein-ligand interaction detected (PLIP)

1 x G2E: (7~{R})-1'-pentylspiro[6~{H}-furo[3,2-f][1,3]benzodioxole-7,3'-indole]-2'-one(Non-covalent)

G2E.4: 11 residues within 4Å: Chain A: Q.360, F.391, I.394, K.1395, T.1684, T.1685, S.1686, I.1733, S.1736, F.1737, V.1741 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.1733, A:F.1737, A:F.1737, A:F.1737, A:V.1741 Hydrogen bonds: A:K.1395

1 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.5: 12 residues within 4Å: Chain A: C.255, V.258, F.259, W.1567, V.1613, R.1620, T.1621, L.1623, F.1624, L.1626, M.1627, E.1758 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.258, A:F.259, A:W.1567, A:V.1613, A:L.1623, A:L.1626 Hydrogen bonds: A:E.1758 Salt bridges: A:R.1620

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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