SMTL ID : 7oo6.1

Mechanosensitive channel MscS solubilized with DDM in closed conformation with added lipid

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

7 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.1: 19 residues within 4Å: Chain A: N.30, A.33, I.37, V.40, I.44, F.80, T.81, A.84, R.88 Chain B: Y.27, N.30, I.31, L.86, V.89, V.91, Q.92, S.95, V.96 Ligands: LMT.4 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:A.33, A:V.40, A:I.44, A:F.80, A:A.84, B:I.31, B:V.89, B:V.89, B:V.91, B:V.91, B:V.96 Salt bridges: A:R.88, A:R.88 Hydrogen bonds: B:N.30 PCW.3: 19 residues within 4Å: Chain B: N.30, A.33, I.37, V.40, I.44, F.80, T.81, A.84, R.88 Chain C: Y.27, N.30, I.31, L.86, V.89, V.91, Q.92, S.95, V.96 Ligands: LMT.6 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:A.33, B:V.40, B:I.44, B:F.80, B:A.84, C:L.86, C:L.86, C:V.89, C:V.89, C:V.91, C:V.91, C:V.96 Salt bridges: B:R.88, B:R.88 Hydrogen bonds: C:N.30 PCW.5: 19 residues within 4Å: Chain C: N.30, A.33, I.37, V.40, I.44, F.80, T.81, A.84, R.88 Chain D: Y.27, N.30, I.31, L.86, V.89, V.91, Q.92, S.95, V.96 Ligands: LMT.8 16 PLIP interactions: 9 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:I.31, D:L.86, D:L.86, D:V.89, D:V.89, D:V.91, D:V.91, D:V.96, C:A.33, C:V.40, C:I.44, C:F.80, C:A.84 Hydrogen bonds: D:N.30 Salt bridges: C:R.88, C:R.88 PCW.7: 19 residues within 4Å: Chain D: N.30, A.33, I.37, V.40, I.44, F.80, T.81, A.84, R.88 Chain E: Y.27, N.30, I.31, L.86, V.89, V.91, Q.92, S.95, V.96 Ligands: LMT.10 15 PLIP interactions: 7 interactions with chain D, 8 interactions with chain E Hydrophobic interactions: D:A.33, D:V.40, D:I.44, D:F.80, D:A.84, E:I.31, E:L.86, E:L.86, E:V.89, E:V.89, E:V.91, E:V.96 Salt bridges: D:R.88, D:R.88 Hydrogen bonds: E:N.30 PCW.9: 19 residues within 4Å: Chain E: N.30, A.33, I.37, V.40, I.44, F.80, T.81, A.84, R.88 Chain F: Y.27, N.30, I.31, L.86, V.89, V.91, Q.92, S.95, V.96 Ligands: LMT.12 16 PLIP interactions: 9 interactions with chain F, 7 interactions with chain E Hydrophobic interactions: F:I.31, F:L.86, F:L.86, F:V.89, F:V.89, F:V.91, F:V.91, F:V.96, E:A.33, E:V.40, E:I.44, E:F.80, E:A.84 Hydrogen bonds: F:N.30 Salt bridges: E:R.88, E:R.88 PCW.11: 19 residues within 4Å: Chain F: N.30, A.33, I.37, V.40, I.44, F.80, T.81, A.84, R.88 Chain G: Y.27, N.30, I.31, L.86, V.89, V.91, Q.92, S.95, V.96 Ligands: LMT.14 16 PLIP interactions: 9 interactions with chain G, 7 interactions with chain F Hydrophobic interactions: G:I.31, G:L.86, G:L.86, G:V.89, G:V.89, G:V.91, G:V.91, G:V.96, F:A.33, F:V.40, F:I.44, F:F.80, F:A.84 Hydrogen bonds: G:N.30 Salt bridges: F:R.88, F:R.88 PCW.13: 19 residues within 4Å: Chain A: Y.27, N.30, I.31, L.86, V.89, V.91, Q.92, S.95, V.96 Chain G: N.30, A.33, I.37, V.40, I.44, F.80, T.81, A.84, R.88 Ligands: LMT.2 16 PLIP interactions: 7 interactions with chain G, 9 interactions with chain A Hydrophobic interactions: G:A.33, G:V.40, G:I.44, G:F.80, G:A.84, A:I.31, A:L.86, A:L.86, A:V.89, A:V.89, A:V.91, A:V.91, A:V.96 Salt bridges: G:R.88, G:R.88 Hydrogen bonds: A:N.30

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

LMT.2: 14 residues within 4Å: Chain A: G.87, G.90, V.91, Q.92, T.93, A.94, A.98, A.102 Chain B: Q.92 Chain G: G.101, L.105 Ligands: LMT.4, PCW.13, LMT.14 7 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A, 1 interactions with chain G Hydrogen bonds: B:Q.92, A:G.90, A:T.93, A:T.93, A:A.94 Hydrophobic interactions: A:A.102, G:L.105 LMT.4: 14 residues within 4Å: Chain A: G.101, L.105 Chain B: G.87, G.90, V.91, Q.92, T.93, A.94, A.98, A.102 Chain C: Q.92 Ligands: PCW.1, LMT.2, LMT.6 7 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:L.105, B:A.102 Hydrogen bonds: B:G.90, B:T.93, B:T.93, B:A.94, C:Q.92 LMT.6: 14 residues within 4Å: Chain B: G.101, L.105 Chain C: G.87, G.90, V.91, Q.92, T.93, A.94, A.98, A.102 Chain D: Q.92 Ligands: PCW.3, LMT.4, LMT.8 7 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:A.102, B:L.105 Hydrogen bonds: C:G.90, C:T.93, C:T.93, C:A.94, D:Q.92 LMT.8: 14 residues within 4Å: Chain C: G.101, L.105 Chain D: G.87, G.90, V.91, Q.92, T.93, A.94, A.98, A.102 Chain E: Q.92 Ligands: PCW.5, LMT.6, LMT.10 7 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: D:A.102, C:L.105 Hydrogen bonds: D:G.90, D:T.93, D:T.93, D:A.94, E:Q.92 LMT.10: 14 residues within 4Å: Chain D: G.101, L.105 Chain E: G.87, G.90, V.91, Q.92, T.93, A.94, A.98, A.102 Chain F: Q.92 Ligands: PCW.7, LMT.8, LMT.12 7 PLIP interactions: 1 interactions with chain F, 5 interactions with chain E, 1 interactions with chain D Hydrogen bonds: F:Q.92, E:G.90, E:T.93, E:T.93, E:A.94 Hydrophobic interactions: E:A.102, D:L.105 LMT.12: 14 residues within 4Å: Chain E: G.101, L.105 Chain F: G.87, G.90, V.91, Q.92, T.93, A.94, A.98, A.102 Chain G: Q.92 Ligands: PCW.9, LMT.10, LMT.14 7 PLIP interactions: 1 interactions with chain G, 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: G:Q.92, F:G.90, F:T.93, F:T.93, F:A.94 Hydrophobic interactions: F:A.102, E:L.105 LMT.14: 14 residues within 4Å: Chain A: Q.92 Chain F: G.101, L.105 Chain G: G.87, G.90, V.91, Q.92, T.93, A.94, A.98, A.102 Ligands: LMT.2, PCW.11, LMT.12 7 PLIP interactions: 5 interactions with chain G, 1 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: G:A.102, F:L.105 Hydrogen bonds: G:G.90, G:T.93, G:T.93, G:A.94, A:Q.92

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
B

C
C

D
D

E
E

F
F

G
G

Membrane

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

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