SMTL ID : 6n4i.1

Structural basis of Nav1.7 inhibition by a gating-modifier spider toxin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.54 Å

Oligo State

hetero-4-4-mer

Ligands

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

6OU.1: 11 residues within 4Å: Chain A: M.158, T.159, F.162, G.185, E.186, F.188 Chain D: M.209, W.216, I.220, F.224 Ligands: 6OU.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.162, A:F.188, D:F.224, D:F.224 Hydrogen bonds: A:G.185 6OU.2: 3 residues within 4Å: Chain A: M.49, H.51 Chain D: T.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.51 Salt bridges: A:H.51 6OU.3: 7 residues within 4Å: Chain A: L.172, F.173, Y.212, Y.214, A.215 Chain B: L.116, S.117 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.117, B:S.117 6OU.4: 10 residues within 4Å: Chain A: M.209, W.216, F.224 Chain B: M.158, T.159, F.162, G.185, E.186, F.188, Y.189 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.216, B:F.162 6OU.5: 5 residues within 4Å: Chain A: T.183 Chain B: L.45, M.49, H.51 Ligands: 6OU.1 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.45 Salt bridges: B:H.51 6OU.6: 7 residues within 4Å: Chain B: L.172, F.173, Y.212, P.213, Y.214 Chain C: L.116, S.117 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.117 6OU.7: 12 residues within 4Å: Chain B: M.209, W.216, I.220, F.224 Chain C: I.155, M.158, T.159, F.162, G.185, E.186, F.188, Y.189 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.155, C:F.162, C:F.162, B:F.224, B:F.224 Hydrogen bonds: C:E.186 6OU.8: 2 residues within 4Å: Chain C: M.49, H.51 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.51 6OU.9: 9 residues within 4Å: Chain C: W.216, I.220, F.224 Chain D: M.158, T.159, F.162, G.185, E.186, F.188 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.220, C:F.224, D:F.162 Hydrogen bonds: C:W.216 6OU.10: 2 residues within 4Å: Chain D: M.49, H.51 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.51 Salt bridges: D:H.51 6OU.11: 7 residues within 4Å: Chain C: L.172, Y.212, P.213, Y.214, A.215 Chain D: G.115, L.116 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.115 6OU.12: 8 residues within 4Å: Chain A: L.116, S.117 Chain D: L.172, F.173, V.211, Y.212, P.213, Y.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.117 6OU.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 6OU.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 6OU.15: 1 residues within 4Å: Chain F: T.8 No protein-ligand interaction detected (PLIP) 6OU.16: 2 residues within 4Å: Chain C: I.64 Chain G: T.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, H. et al., Structural Basis of Nav1.7 Inhibition by a Gating-Modifier Spider Toxin. Cell (2019)

Release Date

2019-01-23

Peptides

Nav1.7 VSD2-NavAb channel chimera protein: ABCD
Beta/omega-theraphotoxin-Tp2a: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Nav1.7 VSD2-NavAb channel chimera protein

Beta/omega-theraphotoxin-Tp2a

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