SMTL ID : 7onj.1

Mechanosensitive channel MscS solubilized with LMNG in open conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

7 x PEE: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.1: 15 residues within 4Å: Chain A: V.52, L.55, M.56, R.59, I.61, V.73, F.80 Chain C: L.72, G.76, L.100, A.103 Chain D: A.102 Ligands: LMT.19, AV0.20, LMT.26 8 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:V.52, A:V.73, A:F.80, C:L.100, C:A.103, D:A.102 Salt bridges: A:R.59, A:R.59 PEE.12: 15 residues within 4Å: Chain A: L.72, Y.75, G.76, L.100, A.103 Chain B: V.52, L.55, M.56, R.59, I.61, V.73, F.80 Ligands: LMT.6, AV0.7, LMT.8 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.52, B:V.73, B:F.80, A:Y.75, A:L.100 Salt bridges: B:R.59, B:R.59 PEE.21: 16 residues within 4Å: Chain C: V.52, L.55, M.56, R.59, I.61, V.73, F.80 Chain D: L.72, G.76, L.100, A.103 Chain E: A.102, A.103 Ligands: LMT.28, AV0.29, LMT.35 8 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: C:V.52, C:V.73, C:F.80, D:L.100, D:A.103, E:A.102 Salt bridges: C:R.59, C:R.59 PEE.30: 15 residues within 4Å: Chain D: V.52, L.55, M.56, R.59, I.61, V.73, F.80 Chain E: L.72, Y.75, G.76, L.100, A.103 Ligands: LMT.37, AV0.38, LMT.44 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:V.52, D:V.73, D:F.80, E:Y.75, E:L.100 Salt bridges: D:R.59, D:R.59 PEE.39: 17 residues within 4Å: Chain E: V.52, L.55, M.56, R.59, I.61, V.73, F.80 Chain F: L.72, Y.75, G.76, L.100, A.103 Chain G: A.102, A.103 Ligands: LMT.46, AV0.47, LMT.53 9 PLIP interactions: 5 interactions with chain E, 1 interactions with chain G, 3 interactions with chain F Hydrophobic interactions: E:V.52, E:V.73, E:F.80, G:A.102, F:Y.75, F:L.100, F:A.103 Salt bridges: E:R.59, E:R.59 PEE.48: 15 residues within 4Å: Chain F: V.52, L.55, M.56, R.59, I.61, V.73, F.80 Chain G: L.72, Y.75, G.76, L.100, A.103 Ligands: LMT.55, LMT.57, AV0.58 9 PLIP interactions: 5 interactions with chain F, 4 interactions with chain G Hydrophobic interactions: F:V.52, F:V.73, F:F.80, G:L.72, G:Y.75, G:L.100, G:A.103 Salt bridges: F:R.59, F:R.59 PEE.59: 17 residues within 4Å: Chain A: A.102, A.103 Chain B: L.72, Y.75, G.76, L.100, A.103 Chain G: V.52, L.55, M.56, R.59, I.61, V.73, F.80 Ligands: LMT.10, LMT.17, AV0.18 7 PLIP interactions: 5 interactions with chain G, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: G:V.52, G:V.73, G:F.80, A:A.102, B:L.100 Salt bridges: G:R.59, G:R.59

21 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.2: 11 residues within 4Å: Chain A: T.93, A.94, I.97, A.98 Chain B: I.97, G.101, A.102 Chain C: A.94 Ligands: LMT.13, LMT.22, LMT.55 Ligand excluded by PLIP LMT.6: 10 residues within 4Å: Chain A: L.42, R.74, Y.75, I.78, L.82 Chain B: L.55, R.59 Chain C: A.98, A.102 Ligands: PEE.12 Ligand excluded by PLIP LMT.8: 14 residues within 4Å: Chain A: G.101, G.104, L.105, L.109, Q.112, S.116 Chain C: A.102, L.105, L.109, Q.112 Ligands: LMT.10, PEE.12, LMT.26, LMT.31 Ligand excluded by PLIP LMT.10: 15 residues within 4Å: Chain A: A.102, L.105, L.109, Q.112 Chain B: G.101, G.104, L.105, G.108, L.109, Q.112, S.116 Ligands: LMT.8, LMT.22, LMT.55, PEE.59 Ligand excluded by PLIP LMT.13: 9 residues within 4Å: Chain A: A.94 Chain B: T.93, A.94, I.97, A.98 Chain G: A.102 Ligands: LMT.2, LMT.53, LMT.60 Ligand excluded by PLIP LMT.17: 11 residues within 4Å: Chain A: A.98, A.102 Chain B: L.42, R.74, Y.75, I.78, L.100, G.101 Chain G: L.55, R.59 Ligands: PEE.59 Ligand excluded by PLIP LMT.19: 10 residues within 4Å: Chain A: L.55, R.59 Chain C: L.42, R.74, Y.75, I.78, L.100, G.101 Chain D: A.102 Ligands: PEE.1 Ligand excluded by PLIP LMT.22: 11 residues within 4Å: Chain A: I.97, G.101, A.102 Chain C: T.93, A.94, I.97, A.98 Chain D: A.94 Ligands: LMT.2, LMT.10, LMT.31 Ligand excluded by PLIP LMT.26: 14 residues within 4Å: Chain C: G.101, G.104, L.105, L.109, Q.112, S.116 Chain D: A.102, L.105, L.109, Q.112 Ligands: PEE.1, LMT.8, LMT.35, LMT.40 Ligand excluded by PLIP LMT.28: 11 residues within 4Å: Chain C: L.55, R.59 Chain D: L.42, R.74, Y.75, I.78, L.100, G.101 Chain E: A.98, A.102 Ligands: PEE.21 Ligand excluded by PLIP LMT.31: 11 residues within 4Å: Chain C: I.97, G.101, A.102 Chain D: T.93, A.94, I.97, A.98 Chain E: A.94 Ligands: LMT.8, LMT.22, LMT.40 Ligand excluded by PLIP LMT.35: 15 residues within 4Å: Chain D: G.101, G.104, L.105, G.108, L.109, Q.112, S.116 Chain E: A.102, L.105, L.109, Q.112 Ligands: PEE.21, LMT.26, LMT.44, LMT.49 Ligand excluded by PLIP LMT.37: 11 residues within 4Å: Chain D: L.55, R.59 Chain E: L.42, R.74, Y.75, I.78, L.82, L.100, G.101 Chain F: A.102 Ligands: PEE.30 Ligand excluded by PLIP LMT.40: 11 residues within 4Å: Chain D: I.97, G.101, A.102 Chain E: T.93, A.94, I.97, A.98 Chain F: A.94 Ligands: LMT.26, LMT.31, LMT.49 Ligand excluded by PLIP LMT.44: 14 residues within 4Å: Chain E: G.101, G.104, L.105, L.109, Q.112, S.116 Chain F: A.102, L.105, L.109, Q.112 Ligands: PEE.30, LMT.35, LMT.53, LMT.60 Ligand excluded by PLIP LMT.46: 11 residues within 4Å: Chain E: L.55, R.59 Chain F: L.42, R.74, Y.75, I.78, L.100, G.101 Chain G: A.98, A.102 Ligands: PEE.39 Ligand excluded by PLIP LMT.49: 11 residues within 4Å: Chain E: I.97, G.101, A.102 Chain F: T.93, A.94, I.97, A.98 Chain G: A.94 Ligands: LMT.35, LMT.40, LMT.60 Ligand excluded by PLIP LMT.53: 15 residues within 4Å: Chain F: G.101, G.104, L.105, G.108, L.109, Q.112, S.116 Chain G: A.102, L.105, L.109, Q.112 Ligands: LMT.13, PEE.39, LMT.44, LMT.55 Ligand excluded by PLIP LMT.55: 14 residues within 4Å: Chain B: A.102, L.105, L.109, Q.112 Chain G: G.101, G.104, L.105, L.109, Q.112, S.116 Ligands: LMT.2, LMT.10, PEE.48, LMT.53 Ligand excluded by PLIP LMT.57: 9 residues within 4Å: Chain B: A.102 Chain F: L.55, R.59 Chain G: L.42, R.74, Y.75, I.78, L.100 Ligands: PEE.48 Ligand excluded by PLIP LMT.60: 12 residues within 4Å: Chain B: A.94 Chain F: I.97, A.98, G.101, A.102 Chain G: T.93, A.94, I.97, A.98 Ligands: LMT.13, LMT.44, LMT.49 Ligand excluded by PLIP

35 x AV0: 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside(Non-covalent)

AV0.3: 13 residues within 4Å: Chain A: A.119, L.123, M.126, F.127 Chain C: F.68, L.111, S.114, L.115, L.118, Q.149, I.150, F.151 Ligands: AV0.20 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.68, C:L.111, C:F.151, A:A.119 Hydrogen bonds: C:Q.149, A:F.127 AV0.4: 9 residues within 4Å: Chain A: Y.27, N.30, I.31, V.89, G.90 Chain B: I.44, A.84 Ligands: AV0.5, AV0.25 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.27, A:I.31, B:I.44, B:A.84 Hydrogen bonds: A:N.30 AV0.5: 10 residues within 4Å: Chain A: Y.27, Q.92 Chain B: A.36, V.40, G.87, R.88, V.91 Ligands: AV0.4, AV0.11, AV0.15 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.27, A:Y.27, A:Y.27, B:A.36, B:V.40 Hydrogen bonds: A:Y.27, A:Q.92, B:G.87 Salt bridges: B:R.88 AV0.7: 17 residues within 4Å: Chain A: R.74, Y.75, G.108, A.110, L.111, L.115 Chain B: K.60, I.61, D.62, T.64, V.65, F.68, L.69, L.118, A.119 Ligands: PEE.12, AV0.14 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Y.75, A:L.111, A:L.115, B:T.64, B:F.68, B:F.68, B:L.69, B:L.118 Hydrogen bonds: A:R.74, B:K.60, B:D.62 Water bridges: A:R.74 AV0.9: 4 residues within 4Å: Chain A: V.29, R.88 Chain C: L.23 Ligands: AV0.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.29 Hydrogen bonds: A:R.88 AV0.11: 4 residues within 4Å: Chain A: L.23 Chain B: V.29, R.88 Ligands: AV0.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.29 Hydrogen bonds: B:R.88, B:R.88 AV0.14: 12 residues within 4Å: Chain A: F.68, L.111, L.115, L.118, Q.149, I.150, F.151 Chain B: A.119, L.123, M.126, F.127 Ligands: AV0.7 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.119, A:F.68, A:L.111, A:L.118, A:F.151 Hydrogen bonds: B:F.127 AV0.15: 9 residues within 4Å: Chain B: Y.27, N.30, I.31, V.89, G.90 Chain G: I.44, A.84 Ligands: AV0.5, AV0.16 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain G Hydrophobic interactions: B:Y.27, B:I.31, G:I.44, G:A.84 Hydrogen bonds: B:N.30 AV0.16: 9 residues within 4Å: Chain B: Y.27, Q.92 Chain G: A.36, V.40, G.87, R.88 Ligands: AV0.15, AV0.56, AV0.62 9 PLIP interactions: 4 interactions with chain G, 5 interactions with chain B Hydrophobic interactions: G:A.36, G:V.40, B:Y.27, B:Y.27, B:Y.27 Hydrogen bonds: G:G.87, B:Y.27, B:Q.92 Salt bridges: G:R.88 AV0.18: 17 residues within 4Å: Chain B: R.74, Y.75, G.108, A.110, L.111, L.115 Chain G: K.60, I.61, D.62, T.64, V.65, F.68, L.69, L.118, A.119 Ligands: PEE.59, AV0.61 13 PLIP interactions: 7 interactions with chain G, 6 interactions with chain B Hydrophobic interactions: G:T.64, G:F.68, G:F.68, G:L.69, G:L.118, B:Y.75, B:L.111, B:L.115 Hydrogen bonds: G:K.60, G:D.62, B:R.74 Water bridges: B:D.67, B:R.74 AV0.20: 17 residues within 4Å: Chain A: K.60, I.61, D.62, T.64, V.65, F.68, L.69, L.118, A.119 Chain C: R.74, Y.75, G.108, A.110, L.111, L.115 Ligands: PEE.1, AV0.3 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:T.64, A:F.68, A:F.68, A:L.69, A:L.118, C:Y.75, C:L.111, C:L.115 Hydrogen bonds: A:K.60, A:D.62, C:R.74 Water bridges: C:D.67, C:R.74 AV0.23: 13 residues within 4Å: Chain C: A.119, L.123, M.126, F.127 Chain D: F.68, L.111, S.114, L.115, L.118, Q.149, I.150, F.151 Ligands: AV0.29 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:A.119, D:F.68, D:L.111, D:L.115, D:I.150, D:F.151 Hydrogen bonds: C:F.127, D:Q.149 AV0.24: 6 residues within 4Å: Chain C: Y.27, N.30, I.31, V.89, G.90 Ligands: AV0.25 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.27, C:I.31 Hydrogen bonds: C:N.30 AV0.25: 9 residues within 4Å: Chain A: A.36, V.40, G.87, R.88 Chain C: Y.27, Q.92 Ligands: AV0.4, AV0.9, AV0.24 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:A.36, A:V.40, C:Y.27, C:Y.27, C:Y.27 Hydrogen bonds: A:G.87, C:Y.27, C:Q.92 Salt bridges: A:R.88 AV0.27: 4 residues within 4Å: Chain C: V.29, R.88 Chain D: L.23 Ligands: AV0.34 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.29 Hydrogen bonds: C:R.88, C:R.88 AV0.29: 17 residues within 4Å: Chain C: K.60, I.61, D.62, T.64, V.65, F.68, L.69, L.118, A.119 Chain D: R.74, Y.75, G.108, A.110, L.111, L.115 Ligands: PEE.21, AV0.23 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:Y.75, D:L.111, D:L.115, C:T.64, C:F.68, C:F.68, C:L.69, C:L.118 Hydrogen bonds: D:R.74, C:K.60, C:D.62 Water bridges: D:D.67, D:R.74 AV0.32: 13 residues within 4Å: Chain D: A.119, L.123, M.126, F.127 Chain E: F.68, L.111, S.114, L.115, L.118, Q.149, I.150, F.151 Ligands: AV0.38 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:F.68, E:L.111, E:L.118, E:F.151, D:A.119 Hydrogen bonds: D:F.127 AV0.33: 8 residues within 4Å: Chain C: I.44 Chain D: Y.27, N.30, I.31, V.89, G.90 Ligands: AV0.34, AV0.43 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.27, D:I.31, C:I.44 Hydrogen bonds: D:N.30 AV0.34: 8 residues within 4Å: Chain C: A.36, V.40, G.87, R.88 Chain D: Y.27, Q.92 Ligands: AV0.27, AV0.33 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.27, D:Y.27, D:Y.27, C:A.36, C:V.40 Hydrogen bonds: D:Y.27, D:Q.92, C:G.87 Salt bridges: C:R.88 AV0.36: 5 residues within 4Å: Chain D: V.29, A.33, R.88 Chain E: L.23 Ligands: AV0.43 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.29, D:A.33 Hydrogen bonds: D:R.88, D:R.88 AV0.38: 17 residues within 4Å: Chain D: K.60, I.61, D.62, T.64, V.65, F.68, L.69, L.118, A.119 Chain E: R.74, Y.75, G.108, A.110, L.111, L.115 Ligands: PEE.30, AV0.32 13 PLIP interactions: 6 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:Y.75, E:L.111, E:L.115, D:T.64, D:F.68, D:F.68, D:L.69, D:L.118 Hydrogen bonds: E:R.74, D:K.60, D:D.62 Water bridges: E:D.67, E:R.74 AV0.41: 13 residues within 4Å: Chain E: A.119, L.123, M.126, F.127 Chain F: F.68, L.111, S.114, L.115, L.118, Q.149, I.150, F.151 Ligands: AV0.47 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:F.68, F:L.111, F:L.115, F:I.150, F:F.151, E:A.119 Hydrogen bonds: F:Q.149, E:F.127 AV0.42: 9 residues within 4Å: Chain D: I.44, A.84 Chain E: Y.27, N.30, I.31, V.89, G.90 Ligands: AV0.43, AV0.52 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:I.44, D:A.84, E:Y.27, E:I.31 Hydrogen bonds: E:N.30 AV0.43: 9 residues within 4Å: Chain D: A.36, V.40, G.87, R.88 Chain E: Y.27, Q.92 Ligands: AV0.33, AV0.36, AV0.42 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:A.36, D:V.40, E:Y.27, E:Y.27, E:Y.27 Hydrogen bonds: D:G.87, E:Y.27, E:Q.92 Salt bridges: D:R.88 AV0.45: 5 residues within 4Å: Chain E: V.29, A.33, R.88 Chain F: L.23 Ligands: AV0.52 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.29, E:A.33 Hydrogen bonds: E:R.88 AV0.47: 17 residues within 4Å: Chain E: K.60, I.61, D.62, T.64, V.65, F.68, L.69, L.118, A.119 Chain F: R.74, Y.75, G.108, A.110, L.111, L.115 Ligands: PEE.39, AV0.41 13 PLIP interactions: 6 interactions with chain F, 7 interactions with chain E Hydrophobic interactions: F:Y.75, F:L.111, F:L.115, E:T.64, E:F.68, E:F.68, E:L.69, E:L.118 Hydrogen bonds: F:R.74, E:K.60, E:D.62 Water bridges: F:D.67, F:R.74 AV0.50: 13 residues within 4Å: Chain F: A.119, L.123, M.126, F.127 Chain G: F.68, L.111, S.114, L.115, L.118, Q.149, I.150, F.151 Ligands: AV0.58 7 PLIP interactions: 2 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: F:A.119, G:F.68, G:L.111, G:L.115, G:F.151 Hydrogen bonds: F:F.127, G:Q.149 AV0.51: 9 residues within 4Å: Chain E: I.44, A.84 Chain F: Y.27, N.30, I.31, V.89, G.90 Ligands: AV0.52, AV0.63 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Y.27, F:I.31, E:I.44, E:A.84 Hydrogen bonds: F:N.30 AV0.52: 9 residues within 4Å: Chain E: A.36, V.40, G.87, R.88 Chain F: Y.27, Q.92 Ligands: AV0.42, AV0.45, AV0.51 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:A.36, E:V.40, F:Y.27, F:Y.27, F:Y.27 Hydrogen bonds: E:G.87, F:Y.27, F:Q.92 Salt bridges: E:R.88 AV0.54: 4 residues within 4Å: Chain F: V.29, R.88 Chain G: L.23 Ligands: AV0.63 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:V.29 Hydrogen bonds: F:R.88 AV0.56: 5 residues within 4Å: Chain B: L.23 Chain G: V.29, A.33, R.88 Ligands: AV0.16 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:V.29, G:A.33 Hydrogen bonds: G:R.88 AV0.58: 17 residues within 4Å: Chain F: K.60, I.61, D.62, T.64, V.65, F.68, L.69, L.118, A.119 Chain G: R.74, Y.75, G.108, A.110, L.111, L.115 Ligands: PEE.48, AV0.50 13 PLIP interactions: 7 interactions with chain F, 6 interactions with chain G Hydrophobic interactions: F:T.64, F:F.68, F:F.68, F:L.69, F:L.118, G:Y.75, G:L.111, G:L.115 Hydrogen bonds: F:K.60, F:D.62, G:R.74 Water bridges: G:D.67, G:R.74 AV0.61: 13 residues within 4Å: Chain B: F.68, L.111, S.114, L.115, L.118, Q.149, I.150, F.151 Chain G: A.119, L.123, M.126, F.127 Ligands: AV0.18 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain G Hydrophobic interactions: B:F.68, B:L.111, B:F.151, G:A.119 Hydrogen bonds: B:Q.149, G:F.127 AV0.62: 9 residues within 4Å: Chain F: I.44, A.84 Chain G: Y.27, N.30, I.31, V.89, G.90 Ligands: AV0.16, AV0.63 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: G:Y.27, G:I.31, F:I.44, F:A.84 Hydrogen bonds: G:N.30 AV0.63: 9 residues within 4Å: Chain F: A.36, V.40, G.87, R.88 Chain G: Y.27, Q.92 Ligands: AV0.51, AV0.54, AV0.62 9 PLIP interactions: 5 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:Y.27, G:Y.27, G:Y.27, F:A.36, F:V.40 Hydrogen bonds: G:Y.27, G:Q.92, F:G.87 Salt bridges: F:R.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flegler, V.J. et al., Mechanosensitive channel gating by delipidation. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-09-01

Peptides

Mechanosensitive channel of small conductance (MscS): ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

C
B

D
C

E
D

F
E

G
F

Membrane

We predict this structure to be a membrane protein.
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Mechanosensitive channel of small conductance (MscS)

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