SMTL ID : 9gj8.1

Structure of Sticholisin II in large unilamellar vesicles.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

32 x FO4: sphingomyelin(Non-covalent)

FO4.1: 16 residues within 4Å: Chain A: R.51, S.52, A.81, T.82, G.83, V.85, S.103, P.105, F.106, Y.111, Y.131, Y.135, Y.136 Ligands: FO4.2, CLR.5, CLR.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.82 Hydrogen bonds: A:S.52, A:G.83, A:F.106, A:Y.111 pi-Cation interactions: A:Y.111 FO4.2: 6 residues within 4Å: Chain A: R.51, Q.128, Y.131, E.132, Y.136 Ligands: FO4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.128, A:Y.136 Salt bridges: A:R.51, A:E.132 FO4.3: 8 residues within 4Å: Chain A: W.110, Y.111, S.112, W.114, Y.135, Y.136, P.139 Ligands: CLR.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.110, A:W.110, A:W.110, A:Y.111 Hydrogen bonds: A:S.112, A:Y.135 pi-Cation interactions: A:W.114 FO4.8: 21 residues within 4Å: Chain A: V.16, V.20, E.23, V.27, R.29, Y.108, S.163, A.164, G.165 Chain B: A.10, F.14, L.17, L.21, T.54, R.74, D.76, T.77, G.78, P.79 Ligands: CLR.4, CLR.14 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:V.16, A:V.20, A:E.23, B:F.14, B:F.14, B:L.17, B:T.77 Hydrogen bonds: A:R.29, A:R.29, A:G.165, A:E.166, B:T.77, B:T.77 pi-Cation interactions: A:Y.108 Salt bridges: B:R.74, B:D.76 FO4.9: 21 residues within 4Å: Chain B: V.16, V.20, E.23, V.27, R.29, Y.108, S.163, A.164, G.165 Chain C: A.10, F.14, L.17, L.21, T.54, R.74, D.76, T.77, G.78, P.79 Ligands: CLR.13, CLR.22 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:V.16, B:V.20, B:E.23, C:F.14, C:F.14, C:L.17, C:T.77 Hydrogen bonds: B:R.29, B:R.29, B:G.165, C:T.77, C:T.77 pi-Cation interactions: B:Y.108 Salt bridges: C:R.74, C:D.76 FO4.10: 15 residues within 4Å: Chain B: R.51, S.52, A.81, T.82, G.83, V.85, S.103, P.105, F.106, Y.111, Y.131, Y.135, Y.136 Ligands: FO4.11, CLR.15 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.82 Hydrogen bonds: B:S.52, B:G.83, B:F.106, B:Y.111 pi-Cation interactions: B:Y.111 FO4.11: 6 residues within 4Å: Chain B: R.51, Q.128, Y.131, E.132, Y.136 Ligands: FO4.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.128, B:Y.136 Salt bridges: B:R.51, B:E.132 FO4.12: 8 residues within 4Å: Chain B: W.110, Y.111, S.112, W.114, Y.135, Y.136, P.139 Ligands: CLR.16 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.110, B:W.110, B:W.110, B:Y.111 Hydrogen bonds: B:S.112, B:Y.135 pi-Cation interactions: B:W.114 FO4.17: 21 residues within 4Å: Chain C: V.16, V.20, E.23, V.27, R.29, Y.108, S.163, A.164, G.165 Chain D: A.10, F.14, L.17, L.21, T.54, R.74, D.76, T.77, G.78, P.79 Ligands: CLR.21, CLR.30 16 PLIP interactions: 8 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:F.14, D:F.14, D:L.17, D:T.77, C:V.16, C:V.20, C:E.23 Hydrogen bonds: D:T.77, D:T.77, C:R.29, C:R.29, C:G.165, C:E.166 Salt bridges: D:R.74, D:D.76 pi-Cation interactions: C:Y.108 FO4.18: 16 residues within 4Å: Chain C: R.51, S.52, A.81, T.82, G.83, V.85, S.103, P.105, F.106, Y.111, Y.131, Y.135, Y.136 Ligands: FO4.19, CLR.22, CLR.23 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.82 Hydrogen bonds: C:S.52, C:G.83, C:F.106, C:Y.111 pi-Cation interactions: C:Y.111 FO4.19: 6 residues within 4Å: Chain C: R.51, Q.128, Y.131, E.132, Y.136 Ligands: FO4.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.128, C:Y.136 Salt bridges: C:R.51, C:E.132 FO4.20: 8 residues within 4Å: Chain C: W.110, Y.111, S.112, W.114, Y.135, Y.136, P.139 Ligands: CLR.24 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.110, C:W.110, C:W.110, C:Y.111 Hydrogen bonds: C:S.112, C:Y.135 pi-Cation interactions: C:W.114 FO4.25: 21 residues within 4Å: Chain D: V.16, V.20, E.23, V.27, R.29, Y.108, S.163, A.164, G.165 Chain E: A.10, F.14, L.17, L.21, T.54, R.74, D.76, T.77, G.78, P.79 Ligands: CLR.29, CLR.38 15 PLIP interactions: 7 interactions with chain D, 8 interactions with chain E Hydrophobic interactions: D:V.16, D:V.20, D:E.23, E:F.14, E:F.14, E:L.17, E:T.77 Hydrogen bonds: D:R.29, D:R.29, D:G.165, E:T.77, E:T.77 pi-Cation interactions: D:Y.108 Salt bridges: E:R.74, E:D.76 FO4.26: 15 residues within 4Å: Chain D: R.51, S.52, A.81, T.82, G.83, V.85, S.103, P.105, F.106, Y.111, Y.131, Y.135, Y.136 Ligands: FO4.27, CLR.31 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:T.82 Hydrogen bonds: D:S.52, D:G.83, D:F.106, D:Y.111 pi-Cation interactions: D:Y.111 FO4.27: 6 residues within 4Å: Chain D: R.51, Q.128, Y.131, E.132, Y.136 Ligands: FO4.26 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.128, D:Y.136 Salt bridges: D:R.51, D:E.132 FO4.28: 8 residues within 4Å: Chain D: W.110, Y.111, S.112, W.114, Y.135, Y.136, P.139 Ligands: CLR.32 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.110, D:W.110, D:W.110, D:Y.111 Hydrogen bonds: D:S.112, D:Y.135 pi-Cation interactions: D:W.114 FO4.33: 20 residues within 4Å: Chain E: V.16, V.20, E.23, V.27, R.29, Y.108, S.163, A.164, G.165 Chain F: A.10, F.14, L.21, T.54, R.74, D.76, T.77, G.78, P.79 Ligands: CLR.37, CLR.46 15 PLIP interactions: 8 interactions with chain E, 7 interactions with chain F Hydrophobic interactions: E:V.16, E:V.20, E:E.23, F:F.14, F:F.14, F:T.77 Hydrogen bonds: E:R.29, E:R.29, E:G.165, E:E.166, F:T.77, F:T.77 pi-Cation interactions: E:Y.108 Salt bridges: F:R.74, F:D.76 FO4.34: 16 residues within 4Å: Chain E: R.51, S.52, A.81, T.82, G.83, V.85, S.103, P.105, F.106, Y.111, Y.131, Y.135, Y.136 Ligands: FO4.35, CLR.38, CLR.39 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:T.82 Hydrogen bonds: E:S.52, E:G.83, E:F.106, E:Y.111 pi-Cation interactions: E:Y.111 FO4.35: 6 residues within 4Å: Chain E: R.51, Q.128, Y.131, E.132, Y.136 Ligands: FO4.34 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.128, E:Y.136 Salt bridges: E:R.51, E:E.132 FO4.36: 8 residues within 4Å: Chain E: W.110, Y.111, S.112, W.114, Y.135, Y.136, P.139 Ligands: CLR.40 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:W.110, E:W.110, E:W.110, E:Y.111 Hydrogen bonds: E:S.112, E:Y.135 pi-Cation interactions: E:W.114 FO4.41: 21 residues within 4Å: Chain F: V.16, V.20, E.23, V.27, R.29, Y.108, S.163, A.164, G.165 Chain G: A.10, F.14, L.17, L.21, T.54, R.74, D.76, T.77, G.78, P.79 Ligands: CLR.45, CLR.54 15 PLIP interactions: 7 interactions with chain F, 8 interactions with chain G Hydrophobic interactions: F:V.16, F:V.20, F:E.23, G:F.14, G:F.14, G:L.17, G:T.77 Hydrogen bonds: F:R.29, F:R.29, F:G.165, G:T.77, G:T.77 pi-Cation interactions: F:Y.108 Salt bridges: G:R.74, G:D.76 FO4.42: 15 residues within 4Å: Chain F: R.51, S.52, A.81, T.82, G.83, V.85, S.103, P.105, F.106, Y.111, Y.131, Y.135, Y.136 Ligands: FO4.43, CLR.47 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:T.82 Hydrogen bonds: F:S.52, F:G.83, F:F.106, F:Y.111 pi-Cation interactions: F:Y.111 FO4.43: 6 residues within 4Å: Chain F: R.51, Q.128, Y.131, E.132, Y.136 Ligands: FO4.42 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.128, F:Y.136 Salt bridges: F:R.51, F:E.132 FO4.44: 8 residues within 4Å: Chain F: W.110, Y.111, S.112, W.114, Y.135, Y.136, P.139 Ligands: CLR.48 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:W.110, F:W.110, F:W.110, F:Y.111 Hydrogen bonds: F:S.112, F:Y.135 pi-Cation interactions: F:W.114 FO4.49: 21 residues within 4Å: Chain G: V.16, V.20, E.23, V.27, R.29, Y.108, S.163, A.164, G.165 Chain H: A.10, F.14, L.17, L.21, T.54, R.74, D.76, T.77, G.78, P.79 Ligands: CLR.53, CLR.62 16 PLIP interactions: 8 interactions with chain H, 8 interactions with chain G Hydrophobic interactions: H:F.14, H:F.14, H:L.17, H:T.77, G:V.16, G:V.20, G:E.23 Hydrogen bonds: H:T.77, H:T.77, G:R.29, G:R.29, G:G.165, G:E.166 Salt bridges: H:R.74, H:D.76 pi-Cation interactions: G:Y.108 FO4.50: 16 residues within 4Å: Chain G: R.51, S.52, A.81, T.82, G.83, V.85, S.103, P.105, F.106, Y.111, Y.131, Y.135, Y.136 Ligands: FO4.51, CLR.54, CLR.55 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:T.82 Hydrogen bonds: G:S.52, G:G.83, G:F.106, G:Y.111 pi-Cation interactions: G:Y.111 FO4.51: 6 residues within 4Å: Chain G: R.51, Q.128, Y.131, E.132, Y.136 Ligands: FO4.50 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Q.128, G:Y.136 Salt bridges: G:R.51, G:E.132 FO4.52: 8 residues within 4Å: Chain G: W.110, Y.111, S.112, W.114, Y.135, Y.136, P.139 Ligands: CLR.56 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:W.110, G:W.110, G:W.110, G:Y.111 Hydrogen bonds: G:S.112, G:Y.135 pi-Cation interactions: G:W.114 FO4.57: 21 residues within 4Å: Chain A: A.10, F.14, L.17, L.21, T.54, R.74, D.76, T.77, G.78, P.79 Chain H: V.16, V.20, E.23, V.27, R.29, Y.108, S.163, A.164, G.165 Ligands: CLR.5, CLR.61 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain H Hydrophobic interactions: A:F.14, A:F.14, A:L.17, A:T.77, H:V.16, H:V.20, H:E.23 Hydrogen bonds: A:T.77, A:T.77, H:R.29, H:R.29, H:G.165 Salt bridges: A:R.74, A:D.76 pi-Cation interactions: H:Y.108 FO4.58: 15 residues within 4Å: Chain H: R.51, S.52, A.81, T.82, G.83, V.85, S.103, P.105, F.106, Y.111, Y.131, Y.135, Y.136 Ligands: FO4.59, CLR.63 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:T.82 Hydrogen bonds: H:S.52, H:G.83, H:F.106, H:Y.111 pi-Cation interactions: H:Y.111 FO4.59: 6 residues within 4Å: Chain H: R.51, Q.128, Y.131, E.132, Y.136 Ligands: FO4.58 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Q.128, H:Y.136 Salt bridges: H:R.51, H:E.132 FO4.60: 8 residues within 4Å: Chain H: W.110, Y.111, S.112, W.114, Y.135, Y.136, P.139 Ligands: CLR.64 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:W.110, H:W.110, H:W.110, H:Y.111 Hydrogen bonds: H:S.112, H:Y.135 pi-Cation interactions: H:W.114

32 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 10 residues within 4Å: Chain A: V.20, L.24, R.29, F.106, D.107, Y.108, N.109 Ligands: CLR.6, CLR.7, FO4.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.20 Hydrogen bonds: A:R.29, A:Y.108 CLR.5: 8 residues within 4Å: Chain A: T.13, L.21, P.79, V.80, A.81 Ligands: FO4.1, CLR.6, FO4.57 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.13, A:L.21 Hydrogen bonds: A:A.81 CLR.6: 6 residues within 4Å: Chain A: A.81, D.107 Ligands: FO4.1, CLR.4, CLR.5, CLR.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.107, A:D.107 CLR.7: 6 residues within 4Å: Chain A: D.107, N.109, W.110 Ligands: FO4.3, CLR.4, CLR.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.109, A:N.109 CLR.13: 11 residues within 4Å: Chain B: V.20, L.24, V.27, R.29, F.106, D.107, Y.108, N.109 Ligands: FO4.9, CLR.15, CLR.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.20, B:L.24, B:V.27 Hydrogen bonds: B:R.29, B:Y.108 CLR.14: 7 residues within 4Å: Chain B: T.13, L.21, P.79, V.80, A.81 Ligands: FO4.8, CLR.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.13, B:L.21 Hydrogen bonds: B:A.81 CLR.15: 6 residues within 4Å: Chain B: A.81, D.107 Ligands: FO4.10, CLR.13, CLR.14, CLR.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.81 Hydrogen bonds: B:D.107, B:D.107 CLR.16: 6 residues within 4Å: Chain B: D.107, N.109, W.110 Ligands: FO4.12, CLR.13, CLR.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.109, B:N.109 CLR.21: 10 residues within 4Å: Chain C: V.20, L.24, R.29, F.106, D.107, Y.108, N.109 Ligands: FO4.17, CLR.23, CLR.24 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.24 Hydrogen bonds: C:R.29, C:Y.108 CLR.22: 8 residues within 4Å: Chain C: T.13, L.21, P.79, V.80, A.81 Ligands: FO4.9, FO4.18, CLR.23 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.13, C:L.21 Hydrogen bonds: C:A.81 CLR.23: 6 residues within 4Å: Chain C: A.81, D.107 Ligands: FO4.18, CLR.21, CLR.22, CLR.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.107, C:D.107 CLR.24: 6 residues within 4Å: Chain C: D.107, N.109, W.110 Ligands: FO4.20, CLR.21, CLR.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.109, C:N.109 CLR.29: 11 residues within 4Å: Chain D: V.20, L.24, V.27, R.29, F.106, D.107, Y.108, N.109 Ligands: FO4.25, CLR.31, CLR.32 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.20, D:L.24, D:V.27 Hydrogen bonds: D:R.29, D:Y.108 CLR.30: 8 residues within 4Å: Chain D: T.13, L.17, L.21, P.79, V.80, A.81 Ligands: FO4.17, CLR.31 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:T.13, D:L.17, D:L.21 Hydrogen bonds: D:A.81 CLR.31: 6 residues within 4Å: Chain D: A.81, D.107 Ligands: FO4.26, CLR.29, CLR.30, CLR.32 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.81 Hydrogen bonds: D:D.107, D:D.107 CLR.32: 6 residues within 4Å: Chain D: D.107, N.109, W.110 Ligands: FO4.28, CLR.29, CLR.31 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.109, D:N.109 CLR.37: 10 residues within 4Å: Chain E: V.20, L.24, R.29, F.106, D.107, Y.108, N.109 Ligands: FO4.33, CLR.39, CLR.40 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:V.20, E:L.24 Hydrogen bonds: E:R.29, E:Y.108 CLR.38: 9 residues within 4Å: Chain E: T.13, L.17, L.21, P.79, V.80, A.81 Ligands: FO4.25, FO4.34, CLR.39 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:T.13, E:L.17, E:L.21 Hydrogen bonds: E:A.81 CLR.39: 6 residues within 4Å: Chain E: A.81, D.107 Ligands: FO4.34, CLR.37, CLR.38, CLR.40 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.107, E:D.107 CLR.40: 6 residues within 4Å: Chain E: D.107, N.109, W.110 Ligands: FO4.36, CLR.37, CLR.39 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.109, E:N.109 CLR.45: 11 residues within 4Å: Chain F: V.20, L.24, V.27, R.29, F.106, D.107, Y.108, N.109 Ligands: FO4.41, CLR.47, CLR.48 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:V.20, F:L.24, F:V.27 Hydrogen bonds: F:R.29, F:Y.108 CLR.46: 7 residues within 4Å: Chain F: T.13, L.21, P.79, V.80, A.81 Ligands: FO4.33, CLR.47 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:T.13, F:L.21 Hydrogen bonds: F:A.81 CLR.47: 6 residues within 4Å: Chain F: A.81, D.107 Ligands: FO4.42, CLR.45, CLR.46, CLR.48 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:A.81 Hydrogen bonds: F:D.107, F:D.107 CLR.48: 6 residues within 4Å: Chain F: D.107, N.109, W.110 Ligands: FO4.44, CLR.45, CLR.47 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.109, F:N.109 CLR.53: 10 residues within 4Å: Chain G: V.20, L.24, R.29, F.106, D.107, Y.108, N.109 Ligands: FO4.49, CLR.55, CLR.56 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:V.20, G:L.24 Hydrogen bonds: G:R.29, G:Y.108 CLR.54: 9 residues within 4Å: Chain G: T.13, L.17, L.21, P.79, V.80, A.81 Ligands: FO4.41, FO4.50, CLR.55 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:T.13, G:L.17, G:L.21 Hydrogen bonds: G:A.81 CLR.55: 6 residues within 4Å: Chain G: A.81, D.107 Ligands: FO4.50, CLR.53, CLR.54, CLR.56 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.107, G:D.107 CLR.56: 6 residues within 4Å: Chain G: D.107, N.109, W.110 Ligands: FO4.52, CLR.53, CLR.55 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.109, G:N.109 CLR.61: 11 residues within 4Å: Chain H: V.20, L.24, V.27, R.29, F.106, D.107, Y.108, N.109 Ligands: FO4.57, CLR.63, CLR.64 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:V.20, H:L.24, H:V.27 Hydrogen bonds: H:R.29, H:Y.108 CLR.62: 7 residues within 4Å: Chain H: T.13, L.21, P.79, V.80, A.81 Ligands: FO4.49, CLR.63 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:T.13, H:L.21 Hydrogen bonds: H:A.81 CLR.63: 6 residues within 4Å: Chain H: A.81, D.107 Ligands: FO4.58, CLR.61, CLR.62, CLR.64 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:A.81 Hydrogen bonds: H:D.107, H:D.107 CLR.64: 6 residues within 4Å: Chain H: D.107, N.109, W.110 Ligands: FO4.60, CLR.61, CLR.63 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:N.109, H:N.109

Links

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Citation

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

Release Date

2025-10-29

Peptides

DELTA-stichotoxin-She4b: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
E

E
G

F
I

G
J

H
L

Membrane

We predict this structure to be a membrane protein.
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DELTA-stichotoxin-She4b

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