SMTL ID : 6hjz.1 (1 other biounit)

Xray structure of GLIC in complex with succinate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-pentamer

Ligands

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

PLC.1: 11 residues within 4Å: Chain A: R.118, F.121, Y.194, I.198, I.202, L.203, Y.254, I.258, N.307, F.315 Ligands: PLC.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.121, A:F.121, A:Y.194, A:I.198, A:I.202, A:L.203, A:I.258 PLC.2: 7 residues within 4Å: Chain A: F.210, T.214, W.217 Chain B: I.271, T.274, V.275, Y.278 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.210, A:T.214, A:W.217, A:W.217, A:W.217, B:I.271, B:T.274, B:Y.278, B:Y.278 PLC.3: 1 residues within 4Å: Ligands: PLC.1 No protein-ligand interaction detected (PLIP) PLC.13: 10 residues within 4Å: Chain B: R.118, F.121, Y.194, I.198, I.202, Y.254, I.258, N.307, F.315 Ligands: PLC.15 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.121, B:F.121, B:F.121, B:I.198, B:I.202, B:Y.254, B:I.258 Hydrogen bonds: B:R.118 PLC.14: 8 residues within 4Å: Chain B: F.210, T.214, W.217 Chain C: F.267, I.271, T.274, V.275, Y.278 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.210, B:T.214, B:W.217, B:W.217, B:W.217, C:F.267, C:I.271, C:T.274, C:Y.278 PLC.15: 1 residues within 4Å: Ligands: PLC.13 No protein-ligand interaction detected (PLIP) PLC.23: 11 residues within 4Å: Chain C: R.118, F.121, Y.194, I.198, I.202, L.206, Y.254, I.258, N.307, F.315 Ligands: PLC.25 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.121, C:F.121, C:F.121, C:Y.194, C:I.202, C:L.206, C:Y.254, C:I.258 PLC.24: 8 residues within 4Å: Chain C: F.210, T.214, W.217 Chain D: F.267, I.271, T.274, V.275, Y.278 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:F.267, D:I.271, D:T.274, D:Y.278, C:F.210, C:T.214, C:W.217, C:W.217, C:W.217 PLC.25: 1 residues within 4Å: Ligands: PLC.23 No protein-ligand interaction detected (PLIP) PLC.30: 10 residues within 4Å: Chain D: R.118, F.121, Y.194, I.198, I.202, L.206, Y.254, N.307, F.315 Ligands: PLC.32 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.121, D:F.121, D:F.121, D:I.198, D:I.202, D:L.206, D:Y.254 Hydrogen bonds: D:R.118 PLC.31: 8 residues within 4Å: Chain D: F.210, T.214, W.217 Chain E: F.267, I.271, T.274, V.275, Y.278 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:F.210, D:T.214, D:W.217, D:W.217, D:W.217, E:F.267, E:I.271, E:T.274, E:Y.278 PLC.32: 1 residues within 4Å: Ligands: PLC.30 No protein-ligand interaction detected (PLIP) PLC.37: 10 residues within 4Å: Chain E: R.118, F.121, Y.194, I.198, I.202, Y.254, I.258, N.307, F.315 Ligands: PLC.39 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.121, E:F.121, E:F.121, E:I.198, E:Y.254, E:I.258 Hydrogen bonds: E:R.118 PLC.38: 8 residues within 4Å: Chain A: F.267, I.271, T.274, V.275, Y.278 Chain E: F.210, T.214, W.217 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:F.267, A:I.271, A:T.274, A:Y.278, E:F.210, E:T.214, E:W.217, E:W.217, E:W.217 PLC.39: 1 residues within 4Å: Ligands: PLC.37 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.16: 3 residues within 4Å: Chain B: R.77, F.78, R.85 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain C: F.78, A.84, R.85 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain D: R.77, F.78, A.84, R.85 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain E: R.77, 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: I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.71, A:I.73 NA.12: 2 residues within 4Å: Chain A: T.226 Chain B: T.226 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.226, A:T.226 NA.17: 4 residues within 4Å: Chain B: P.68, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.71, B:I.73 NA.27: 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.34: 4 residues within 4Å: Chain D: I.71, W.72, I.73 Ligands: SIN.36 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.73, D:I.73 NA.41: 4 residues within 4Å: Chain E: P.68, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.71, E:I.73

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

LMT.8: 5 residues within 4Å: Ligands: LMT.9, LMT.18, LMT.28, LMT.35, LMT.42 No protein-ligand interaction detected (PLIP) LMT.9: 5 residues within 4Å: Chain A: A.237, I.240 Chain B: T.244 Chain E: A.237 Ligands: LMT.8 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: E:A.237, A:I.240, B:T.244 LMT.18: 7 residues within 4Å: Chain A: A.237 Chain B: A.237, I.240, L.241, T.244 Chain C: T.244 Ligands: LMT.8 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:I.240, B:I.240, B:L.241, A:A.237, C:T.244 LMT.28: 7 residues within 4Å: Chain B: A.237 Chain C: A.237, I.240, L.241, T.244 Chain D: T.244 Ligands: LMT.8 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: B:A.237, D:T.244, C:I.240, C:I.240, C:L.241 LMT.35: 7 residues within 4Å: Chain C: A.237 Chain D: A.237, I.240, L.241, T.244 Chain E: T.244 Ligands: LMT.8 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: D:I.240, D:I.240, D:L.241, C:A.237, E:T.244 LMT.42: 5 residues within 4Å: Chain D: A.237 Chain E: I.240, L.241, T.244 Ligands: LMT.8 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:I.240, E:L.241, D:A.237

10 x SIN: SUCCINIC ACID(Non-covalent)

SIN.10: 9 residues within 4Å: Chain A: R.77, I.131, F.174, L.176, E.181 Chain E: I.25, F.42, R.105, N.152 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:I.131, A:L.176, E:F.42 Hydrogen bonds: A:E.181, E:N.152 Salt bridges: A:R.77, E:R.105 SIN.11: 6 residues within 4Å: Chain A: I.73, P.74, E.75, I.76, R.77, R.85 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:I.76, A:I.76, A:R.77, E:D.88 Salt bridges: A:R.85 SIN.19: 4 residues within 4Å: Chain B: P.74, I.76, R.85, A.87 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.76 Salt bridges: B:R.85, B:R.85 SIN.20: 9 residues within 4Å: Chain B: I.25, F.42, R.105, N.152 Chain C: R.77, I.131, F.174, L.176, E.181 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.42, C:I.131, C:L.176 Hydrogen bonds: B:N.152 Salt bridges: B:R.105, C:R.77 SIN.21: 10 residues within 4Å: Chain A: Y.23, I.25, F.42, R.105, N.152 Chain B: R.77, I.131, F.174, L.176, E.181 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.176, A:I.25, A:F.42 Hydrogen bonds: B:E.181, A:N.152 Salt bridges: B:R.77, A:R.105 SIN.22: 10 residues within 4Å: Chain C: Y.23, I.25, F.42, R.105, N.152 Chain D: R.77, V.79, I.131, L.176, E.181 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:N.152, D:E.181 Salt bridges: C:R.105, D:R.77 Hydrophobic interactions: D:I.131, D:L.176 SIN.29: 5 residues within 4Å: Chain C: P.74, E.75, I.76, R.77, R.85 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:I.76, C:I.76, C:I.76 Salt bridges: C:R.77, C:R.85 SIN.36: 8 residues within 4Å: Chain D: I.73, P.74, E.75, I.76, R.85, Y.102, E.104 Ligands: NA.34 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.73 Hydrogen bonds: D:P.74, D:I.76 Salt bridges: D:R.85 SIN.43: 7 residues within 4Å: Chain E: P.74, E.75, I.76, R.85, A.87, Y.102, E.104 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:I.76, E:Y.102, E:Y.102, E:E.104 Salt bridges: E:R.85 SIN.44: 9 residues within 4Å: Chain D: I.25, F.42, R.105, N.152 Chain E: R.77, I.131, F.174, L.176, E.181 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:I.131, D:F.42 Hydrogen bonds: E:E.181, D:N.152 Salt bridges: E:R.77, D:R.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fourati, Z. et al., Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel. Acta Crystallogr D Struct Biol (2020)

Release Date

2019-09-18

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.
Show / Hide

Proton-gated ion channel

Related Entries With Identical Sequence