SMTL ID : 6f0u.1

GLIC mutant E35A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-pentamer

Ligands

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: R.77, I.131, E.181 Chain E: F.42, R.105 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:F.42, A:I.131 Salt bridges: E:R.105, A:R.77 ACT.8: 7 residues within 4Å: Chain A: L.45, I.73, P.74, E.75, I.76, R.85, Y.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.76 Salt bridges: A:R.85 ACT.11: 5 residues within 4Å: Chain A: F.42, R.105 Chain B: R.77, I.131, E.181 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.131, A:F.42 Hydrogen bonds: B:E.181 Salt bridges: B:R.77, A:R.105 ACT.16: 7 residues within 4Å: Chain B: I.73, P.74, E.75, I.76, R.85, Y.102, E.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.76, B:I.76 Salt bridges: B:R.85 ACT.18: 5 residues within 4Å: Chain B: F.42, R.105 Chain C: R.77, I.131, E.181 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.131 Salt bridges: C:R.77, B:R.105 ACT.23: 7 residues within 4Å: Chain C: I.73, P.74, E.75, I.76, R.85, Y.102, E.104 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.76, C:I.76 Salt bridges: C:R.85 ACT.26: 5 residues within 4Å: Chain C: F.42, R.105 Chain D: R.77, I.131, E.181 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.42, D:I.131 Salt bridges: C:R.105, D:R.77 ACT.31: 4 residues within 4Å: Chain D: I.73, P.74, I.76, R.85 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.76, D:I.76 Salt bridges: D:R.85 ACT.33: 5 residues within 4Å: Chain D: F.42, R.105 Chain E: R.77, I.131, E.181 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:F.42, E:I.131 Salt bridges: D:R.105, E:R.77 ACT.38: 8 residues within 4Å: Chain E: L.45, I.73, P.74, E.75, I.76, R.85, Y.102, E.104 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.76 Salt bridges: E:R.85

10 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.2: 8 residues within 4Å: Chain A: R.118, F.121, Y.194, I.198, I.202, Y.254, N.307, F.315 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.121, A:F.121, A:Y.194, A:I.198, A:I.202, A:Y.254 PLC.3: 9 residues within 4Å: Chain A: F.210, W.213, T.214, W.217 Chain B: F.267, I.271, T.274, V.275, Y.278 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.267, B:I.271, B:I.271, B:T.274, B:Y.278, B:Y.278, A:W.213, A:T.214, A:W.217, A:W.217, A:W.217 PLC.12: 8 residues within 4Å: Chain B: R.118, F.121, Y.194, I.198, I.202, Y.254, N.307, F.315 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.121, B:F.121, B:Y.194, B:I.198, B:I.202 PLC.13: 8 residues within 4Å: Chain B: F.210, W.213, T.214, W.217 Chain C: I.271, T.274, V.275, Y.278 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:W.213, B:T.214, B:W.217, B:W.217, B:W.217, C:I.271, C:I.271, C:T.274, C:V.275, C:Y.278, C:Y.278 PLC.20: 7 residues within 4Å: Chain C: R.118, F.121, Y.194, I.202, Y.254, N.307, F.315 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.121, C:F.121, C:Y.194, C:I.202, C:Y.254 PLC.25: 8 residues within 4Å: Chain C: F.210, W.213, T.214, W.217 Chain D: I.271, T.274, V.275, Y.278 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:I.271, D:I.271, D:T.274, D:Y.278, D:Y.278, C:W.213, C:T.214, C:W.217, C:W.217, C:W.217 PLC.27: 9 residues within 4Å: Chain D: R.118, F.121, Y.194, I.198, I.202, L.206, Y.254, N.307, F.315 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.121, D:F.121, D:Y.194, D:I.198, D:I.202, D:L.206, D:Y.254 PLC.28: 9 residues within 4Å: Chain D: F.210, W.213, T.214, W.217 Chain E: F.267, I.271, T.274, V.275, Y.278 12 PLIP interactions: 7 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:F.267, E:I.271, E:I.271, E:T.274, E:V.275, E:Y.278, E:Y.278, D:W.213, D:T.214, D:W.217, D:W.217, D:W.217 PLC.34: 8 residues within 4Å: Chain E: R.118, F.121, Y.194, I.202, L.206, Y.254, N.307, F.315 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.121, E:F.121, E:Y.194, E:I.202, E:L.206, E:Y.254 PLC.35: 8 residues within 4Å: Chain A: F.267, I.271, V.275, Y.278 Chain E: F.210, W.213, T.214, W.217 10 PLIP interactions: 5 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:W.213, E:T.214, E:W.217, E:W.217, E:W.217, A:F.267, A:I.271, A:V.275, A:Y.278, A:Y.278

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: R.77, F.78, R.85 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: N.139, R.179, L.180 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: A.175 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: R.77, F.78, R.85 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: F.78, A.84, R.85 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain D: R.77, F.78, R.85 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain E: F.78, R.85 Ligand excluded by PLIP

6 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain A: P.68, I.71, I.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.71, A:I.73 NA.15: 3 residues within 4Å: Chain B: P.68, I.71, I.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.73 NA.19: 2 residues within 4Å: Chain C: T.226 Chain D: T.226 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.226, D:T.226, C:T.226 NA.22: 3 residues within 4Å: Chain C: P.68, I.71, I.73 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.71, C:I.73 NA.30: 2 residues within 4Å: Chain D: P.68, I.71 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.71, D:I.73 NA.37: 3 residues within 4Å: Chain E: P.68, I.71, I.73 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.73

6 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-functional Binders)(Non-covalent)

LMT.9: 5 residues within 4Å: Ligands: LMT.10, LMT.17, LMT.24, LMT.32, LMT.39 No protein-ligand interaction detected (PLIP) LMT.10: 7 residues within 4Å: Chain A: A.237, I.240, L.241, T.244 Chain B: T.244 Chain E: A.237 Ligands: LMT.9 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: A:A.237, A:I.240, A:L.241, E:A.237, B:T.244 LMT.17: 7 residues within 4Å: Chain A: A.237 Chain B: I.233, A.237, I.240, L.241, T.244 Ligands: LMT.9 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.237, B:I.233, B:I.240, B:I.240, B:L.241 LMT.24: 8 residues within 4Å: Chain B: A.237 Chain C: I.233, A.237, I.240, T.244 Chain D: T.244 Ligands: LMT.9, LMT.32 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:I.233, C:I.240, C:I.240, B:A.237, D:T.244 LMT.32: 8 residues within 4Å: Chain C: A.237 Chain D: I.233, A.237, I.240, L.241, T.244 Ligands: LMT.9, LMT.24 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.237, D:I.233, D:A.237, D:I.240 LMT.39: 7 residues within 4Å: Chain D: A.237 Chain E: I.233, A.237, I.240, L.241, T.244 Ligands: LMT.9 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:I.233, E:A.237, E:I.240, E:L.241, D:A.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nemecz, A. et al., Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel. PLoS Biol. (2017)

Release Date

2018-01-10

Peptides

Proton-gated ion channel: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Proton-gated ion channel