SMTL ID : 6hzw.1

THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL 2.22 resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.22 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 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:F.42 Salt bridges: E:R.105, A:R.77 ACT.8: 5 residues within 4Å: Chain A: I.73, P.74, I.76, R.85, Y.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.76 Water bridges: A:I.76 Salt bridges: A:R.85 ACT.14: 5 residues within 4Å: Chain A: F.42, R.105 Chain B: R.77, I.131, E.181 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.42 Salt bridges: A:R.105, B:R.77 ACT.19: 6 residues within 4Å: Chain B: I.73, P.74, I.76, R.85, Y.102, E.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.76, B:I.76 Water bridges: B:Y.102 Salt bridges: B:R.85 ACT.24: 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 B, 1 interactions with chain C Hydrophobic interactions: B:F.42 Salt bridges: B:R.105, C:R.77 ACT.29: 6 residues within 4Å: Chain C: I.73, P.74, E.75, I.76, R.85, Y.102 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.76, C:I.76 Salt bridges: C:R.85 ACT.33: 6 residues within 4Å: Chain C: I.25, F.42, R.105 Chain D: R.77, I.131, E.181 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.25, C:F.42 Salt bridges: C:R.105, D:R.77 ACT.38: 5 residues within 4Å: Chain D: I.73, P.74, I.76, R.85, Y.102 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.76, D:I.76 Salt bridges: D:R.85 ACT.42: 5 residues within 4Å: Chain D: F.42, R.105 Chain E: R.77, I.131, E.181 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:F.42 Salt bridges: D:R.105, E:R.77 ACT.47: 6 residues within 4Å: Chain E: I.73, P.74, E.75, I.76, R.85, Y.102 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:I.76, E:I.76 Salt bridges: E:R.85

15 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)(Non-functional Binders)

PLC.2: 8 residues within 4Å: Chain A: R.118, F.121, Y.194, I.198, Y.254, N.307, F.315 Ligands: PLC.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.121, A:F.121, A:I.198, A:Y.254 Hydrogen bonds: A:R.118 PLC.3: 1 residues within 4Å: Ligands: PLC.2 No protein-ligand interaction detected (PLIP) PLC.12: 9 residues within 4Å: Chain A: I.271, T.274, V.275, Y.278, E.282, Q.284, R.287 Chain E: F.210, W.217 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:T.274, A:V.275, E:W.217, E:W.217 Hydrogen bonds: A:Q.284 Salt bridges: A:E.282, A:R.287, A:R.287 PLC.13: 9 residues within 4Å: Chain A: F.210, W.217 Chain B: I.271, T.274, V.275, Y.278, E.282, Q.284, R.287 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.210, A:F.210, A:W.217, A:W.217, A:W.217, B:I.271, B:T.274, B:V.275 Hydrogen bonds: B:Q.284 Salt bridges: B:R.287 PLC.15: 9 residues within 4Å: Chain B: R.118, F.121, Y.194, I.198, Y.254, I.258, N.307, F.315 Ligands: PLC.16 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.121, B:Y.194, B:I.198, B:Y.254, B:I.258 Hydrogen bonds: B:R.118 PLC.16: 1 residues within 4Å: Ligands: PLC.15 No protein-ligand interaction detected (PLIP) PLC.23: 9 residues within 4Å: Chain B: F.210, W.217 Chain C: I.271, T.274, V.275, Y.278, E.282, Q.284, R.287 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.271, C:T.274, C:V.275, B:W.217, B:W.217, B:W.217 Hydrogen bonds: C:Q.284, C:R.287 Salt bridges: C:R.287 PLC.25: 8 residues within 4Å: Chain C: R.118, F.121, Y.194, I.198, Y.254, I.258, N.307, F.315 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.121, C:Y.194, C:I.198, C:Y.254, C:I.258 PLC.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PLC.32: 9 residues within 4Å: Chain C: F.210, W.217 Chain D: I.271, V.275, Y.278, E.282, Q.284, R.287, I.291 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:W.217, C:W.217, D:I.271, D:V.275 Hydrogen bonds: D:Q.284 Salt bridges: D:R.287, D:R.287 PLC.34: 6 residues within 4Å: Chain D: R.118, F.121, Y.194, Y.254, N.307, F.315 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.121, D:F.121, D:Y.254 Hydrogen bonds: D:R.118 PLC.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PLC.41: 9 residues within 4Å: Chain D: F.210, W.217 Chain E: I.271, T.274, V.275, Y.278, E.282, Q.284, R.287 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:W.217, E:I.271, E:T.274, E:V.275 Hydrogen bonds: E:Q.284 Salt bridges: E:R.287, E:R.287 PLC.43: 7 residues within 4Å: Chain E: R.118, F.121, Y.194, I.198, Y.254, N.307, F.315 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.121, E:I.198, E:Y.254 Hydrogen bonds: E:R.118 PLC.44: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain A: F.78, A.84, 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.17: 3 residues within 4Å: Chain B: F.78, A.84, R.85 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain C: F.78, A.84, R.85 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain D: F.78, A.84, R.85 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain E: F.78, A.84, 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.18: 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.22: 2 residues within 4Å: Chain C: T.226 Chain D: T.226 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:T.226, C:T.226, D:T.226 Water bridges: B:T.226 NA.28: 3 residues within 4Å: Chain C: P.68, I.71, I.73 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.68, C:I.73 NA.37: 4 residues within 4Å: Chain D: P.68, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.68, D:I.73 NA.46: 3 residues within 4Å: Chain E: P.68, E.69, I.71 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.69

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

LMT.9: 2 residues within 4Å: Ligands: LMT.20, LMT.48 No protein-ligand interaction detected (PLIP) LMT.10: 2 residues within 4Å: Chain A: A.237 Chain E: A.237 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.237 LMT.11: 4 residues within 4Å: Chain A: R.117, R.118, L.313, F.314 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.314 Hydrogen bonds: A:R.118, A:F.314 LMT.20: 5 residues within 4Å: Chain A: A.237 Chain B: A.237, I.240 Chain C: T.244 Ligands: LMT.9 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:A.237, B:I.240, B:I.240, C:T.244, A:A.237 LMT.21: 7 residues within 4Å: Chain B: R.118, M.252, A.257, F.260, M.261, L.313, F.314 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.260, B:M.261, B:F.314 Hydrogen bonds: B:R.118, B:F.314 LMT.30: 5 residues within 4Å: Chain B: A.237 Chain C: I.233, A.237, I.240 Chain D: T.244 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: B:A.237, D:T.244, C:A.237, C:I.240 LMT.31: 5 residues within 4Å: Chain C: R.117, R.118, M.261, L.313, F.314 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:M.261 Hydrogen bonds: C:R.118, C:F.314 LMT.39: 2 residues within 4Å: Chain D: A.237, I.240 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.237, D:I.240 LMT.40: 5 residues within 4Å: Chain D: R.117, R.118, M.261, L.313, F.314 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:M.261, D:F.314 Hydrogen bonds: D:R.118, D:F.314 LMT.48: 4 residues within 4Å: Chain D: A.237 Chain E: A.237, I.240 Ligands: LMT.9 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:A.237, E:I.240, D:A.237 LMT.49: 5 residues within 4Å: Chain E: R.117, R.118, F.260, L.313, F.314 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.260, E:F.314 Hydrogen bonds: E:R.118, E:F.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, H. et al., Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-12-19

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

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