SMTL ID : 9gki.1

Structure of 5mer pore intermediate of Sticholysin II (StnII) toxin in lipid nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

8 x FO4: sphingomyelin(Non-covalent)

FO4.1: 6 residues within 4Å: Chain A: W.110, Y.111, W.114, Y.135, Y.136, P.139 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.110 Hydrogen bonds: A:Y.135 pi-Cation interactions: A:Y.135 FO4.2: 7 residues within 4Å: Chain A: R.51, S.52, T.82, G.83, V.85, P.105, Y.111 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.111 FO4.3: 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 pi-Cation interactions: C:W.114, C:W.114 FO4.4: 11 residues within 4Å: Chain A: F.106, D.107, Y.108, S.163, A.164, G.165 Chain C: T.54, R.74, D.76, T.77, V.80 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.77, A:D.107 Salt bridges: C:D.76 pi-Cation interactions: A:Y.108 FO4.5: 11 residues within 4Å: Chain C: R.51, A.81, T.82, G.83, V.85, S.103, P.105, F.106, Y.111, Y.131, Y.135 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.83, C:F.106 FO4.6: 4 residues within 4Å: Chain D: W.110, Y.111, W.114, Y.135 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.110 FO4.7: 10 residues within 4Å: Chain D: S.52, A.81, T.82, G.83, V.85, S.103, P.105, Y.111, Y.131, Y.135 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.52, D:S.52, D:G.83 FO4.8: 9 residues within 4Å: Chain E: R.51, S.52, A.81, T.82, G.83, V.85, F.106, Y.111, Y.135 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:Y.111 Hydrogen bonds: E:S.52, E:S.52, E:G.83 pi-Cation interactions: E:Y.111

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

2025-09-17

Peptides

DELTA-stichotoxin-She4b: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
f

C
n

D
v

E
B

DELTA-stichotoxin-She4b

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