SMTL ID : 9gko.1

Structure of 6mer pore intermediate of Sticholysin II (StnII) toxin in lipid nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

7 x FO4: sphingomyelin(Non-covalent)

FO4.1: 5 residues within 4Å: Chain B: W.110, Y.111, W.114, Y.135, P.139 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.110 Hydrogen bonds: B:Y.135 pi-Cation interactions: B:W.114 FO4.2: 6 residues within 4Å: Chain B: R.51, A.81, V.85, F.106, Y.111, Y.135 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.106 Hydrogen bonds: B:A.81, B:Y.111 Salt bridges: B:R.51 FO4.3: 13 residues within 4Å: Chain C: G.53, T.54, R.74, D.76, T.77, G.78, P.79 Chain E: R.29, Y.108, S.163, A.164, G.165, E.166 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain E Hydrogen bonds: C:T.77, C:T.77, C:T.77, E:R.29, E:G.165, E:E.166 Salt bridges: C:D.76, E:R.29 Hydrophobic interactions: E:Y.108 pi-Cation interactions: E:Y.108 FO4.4: 7 residues within 4Å: Chain C: W.110, Y.111, S.112, W.114, Y.135, Y.136, P.139 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.110, C:Y.135, C:Y.136 Hydrogen bonds: C:S.112, C:W.114, C:Y.135 pi-Cation interactions: C:W.114 FO4.5: 7 residues within 4Å: Chain C: R.51, A.81, T.82, Y.111, Y.131, Y.135, Y.136 No protein-ligand interaction detected (PLIP) FO4.6: 8 residues within 4Å: Chain E: G.83, V.85, S.103, F.106, Y.111, Y.131, Y.135, Y.136 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:Y.111 pi-Cation interactions: E:Y.111, E:Y.135 FO4.7: 5 residues within 4Å: Chain E: W.110, Y.111, W.114, Y.135, P.139 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.111 pi-Cation interactions: E:W.114, E:Y.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arranz, R. et al., Elucidating the structure and assembly mechanism of actinoporin pores in complex membrane environments. Sci Adv (2025)

Release Date

2025-10-08

Peptides

DELTA-stichotoxin-She4b: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
n

C
A

D
C

E
D

F
G

DELTA-stichotoxin-She4b

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