SMTL ID : 5iux.1

GLIC-V135C bimane labelled X-ray structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-pentamer

Ligands

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

LMT.1: 13 residues within 4Å: Chain A: D.31, K.33, I.233, A.237, I.240, T.244, N.245 Chain B: K.33, T.244 Chain E: A.237 Ligands: LMT.6, LMT.12, LMT.36 8 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: B:T.244, E:A.237, A:I.233, A:A.237, A:I.240 Salt bridges: B:K.33 Hydrogen bonds: A:D.31, A:N.245 LMT.6: 17 residues within 4Å: Chain A: T.226, V.229, S.230, I.233 Chain B: S.230, I.233 Chain C: S.230, I.233 Chain D: I.233 Chain E: T.226, S.230, I.233 Ligands: LMT.1, LMT.12, LMT.19, LMT.35, LMT.36 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 interactions with chain E, 1 interactions with chain C Hydrogen bonds: B:S.230, B:S.230, A:S.230, E:S.230, E:S.230, C:S.230 LMT.12: 13 residues within 4Å: Chain A: A.237 Chain B: D.31, K.33, A.237, I.240, L.241, T.244, N.245 Chain C: K.33, T.244 Ligands: LMT.1, LMT.6, LMT.19 12 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:A.237, B:I.240, B:L.241, A:A.237 Hydrogen bonds: B:D.31, B:T.244, B:T.244, C:K.33 Water bridges: B:L.30, B:D.31, B:D.32, B:D.32 LMT.19: 10 residues within 4Å: Chain B: A.237 Chain C: I.233, A.237, I.240, T.244, N.245 Chain D: K.33 Ligands: LMT.6, LMT.12, LMT.35 8 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:I.233, C:I.240, C:I.240, B:A.237 Hydrogen bonds: C:T.244, D:K.33, D:K.33 Salt bridges: D:K.33 LMT.35: 14 residues within 4Å: Chain C: A.237 Chain D: I.233, I.236, A.237, I.240, L.241, T.244, N.245 Chain E: K.33, I.240, T.244 Ligands: LMT.6, LMT.19, LMT.36 11 PLIP interactions: 4 interactions with chain E, 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: E:I.240, D:I.233, D:I.236, D:A.237, D:I.240, D:L.241, C:A.237 Hydrogen bonds: E:K.33, E:T.244, D:T.244 Salt bridges: E:K.33 LMT.36: 13 residues within 4Å: Chain D: A.237 Chain E: D.31, D.32, K.33, I.233, A.237, I.240, L.241, T.244, N.245 Ligands: LMT.1, LMT.6, LMT.35 11 PLIP interactions: 9 interactions with chain E, 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: E:I.233, E:A.237, E:I.240, D:A.237 Hydrogen bonds: E:D.32, E:D.32, E:K.33, E:T.244, E:T.244, E:N.245 Water bridges: A:K.248

15 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.2: 11 residues within 4Å: Chain A: R.118, F.121, Y.194, I.202, L.203, L.206, Y.254, F.303, N.307, F.315 Ligands: PC1.11 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.121, A:F.121, A:F.121, A:Y.194, A:I.202, A:L.203, A:L.206, A:Y.254, A:F.303, A:N.307 Hydrogen bonds: A:R.118 PC1.3: 10 residues within 4Å: Chain A: F.265, V.268, R.287, I.291, A.294, S.295, A.298, F.299, V.302 Ligands: PC1.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.265, A:F.265, A:A.294, A:A.298, A:F.299, A:V.302, A:V.302 Salt bridges: A:R.287 PC1.4: 11 residues within 4Å: Chain A: I.271, V.275, Y.278, E.282 Chain E: F.210, W.217, R.296, P.300, F.303, L.304 Ligands: PC1.3 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:F.210, E:F.210, E:F.210, E:F.210, E:W.217, E:W.217, E:F.303, E:L.304, E:L.304, A:I.271, A:I.271, A:V.275 Hydrogen bonds: A:Q.284 PC1.11: 14 residues within 4Å: Chain A: F.210, W.213, W.217, R.296, P.300, F.303, L.304 Chain B: I.271, V.275, Y.278, L.279, E.282 Ligands: PC1.2, PC1.14 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.210, A:F.210, A:W.213, A:W.217, A:W.217, A:F.303, A:L.304, B:I.271, B:Y.278 PC1.13: 10 residues within 4Å: Chain B: R.118, F.121, Y.194, I.202, L.203, L.206, Y.254, I.258, N.307, F.315 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.121, B:F.121, B:I.202, B:L.203, B:L.206, B:I.258 Hydrogen bonds: B:R.118 PC1.14: 12 residues within 4Å: Chain B: F.265, V.268, I.271, E.272, R.287, I.291, A.294, S.295, A.298, F.299, V.302 Ligands: PC1.11 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.265, B:F.265, B:V.268, B:V.268, B:I.271, B:E.272, B:I.291, B:A.298, B:V.302 Salt bridges: B:R.287 PC1.18: 14 residues within 4Å: Chain B: F.210, W.213, W.217, P.300, F.303 Chain C: F.267, I.271, T.274, V.275, Y.278, L.279, E.282, R.287 Ligands: PC1.21 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:W.213, B:W.217, B:W.217, B:W.217, B:P.300, B:F.303, C:F.267, C:I.271, C:T.274, C:V.275 PC1.20: 13 residues within 4Å: Chain C: R.118, F.121, S.123, E.163, S.191, Y.194, I.198, I.202, L.206, Y.254, I.258, N.307, F.315 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.121, C:Y.194, C:I.198, C:I.202, C:L.206, C:Y.254, C:I.258, C:F.315 Hydrogen bonds: C:R.118, C:Y.194 Salt bridges: C:E.163 PC1.21: 11 residues within 4Å: Chain C: F.265, V.268, E.272, R.287, S.290, I.291, A.294, S.295, A.298, F.299 Ligands: PC1.18 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.265, C:F.265, C:V.268, C:V.268, C:I.291, C:A.294, C:A.298, C:F.299 Salt bridges: C:R.287 PC1.26: 14 residues within 4Å: Chain C: F.210, T.214, W.217, R.296, P.300, F.303, L.304 Chain D: I.271, V.275, Y.278, L.279, E.282, Q.284 Ligands: PC1.28 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:I.271, D:Y.278, C:F.210, C:F.210, C:F.210, C:T.214, C:W.217, C:W.217, C:F.303, C:L.304 Hydrogen bonds: D:Q.284 PC1.27: 11 residues within 4Å: Chain D: R.118, F.121, Y.194, I.202, L.203, L.206, Y.254, I.258, F.303, N.307, F.315 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.121, D:F.121, D:F.121, D:I.202, D:L.203, D:L.206, D:Y.254, D:I.258, D:F.303 Hydrogen bonds: D:Y.194 Salt bridges: D:R.118 PC1.28: 10 residues within 4Å: Chain D: F.265, V.268, E.272, R.287, I.291, A.294, S.295, A.298, V.302 Ligands: PC1.26 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.265, D:F.265, D:V.268, D:E.272, D:I.291, D:A.298, D:V.302 Salt bridges: D:R.287 PC1.37: 16 residues within 4Å: Chain D: F.210, W.213, T.214, W.217, R.296, P.300, F.303, L.304 Chain E: I.271, T.274, V.275, Y.278, L.279, E.282, Q.284 Ligands: PC1.39 16 PLIP interactions: 11 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:F.210, D:F.210, D:F.210, D:F.210, D:W.213, D:W.213, D:W.217, D:W.217, D:W.217, D:F.303, D:L.304, E:I.271, E:I.271, E:T.274, E:V.275 Hydrogen bonds: E:Q.284 PC1.38: 11 residues within 4Å: Chain E: R.118, F.121, S.191, Y.194, I.198, L.203, L.206, Y.254, I.258, N.307, F.315 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:F.121, E:F.121, E:I.198, E:I.198, E:L.203, E:L.206, E:I.258 Hydrogen bonds: E:Y.194 Salt bridges: E:R.118 PC1.39: 12 residues within 4Å: Chain E: F.265, V.268, I.271, E.272, R.287, I.291, A.294, S.295, A.298, F.299, V.302 Ligands: PC1.37 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.265, E:V.268, E:I.271, E:E.272, E:A.294, E:V.302, E:V.302 Salt bridges: E:R.287

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

ACT.5: 7 residues within 4Å: Chain A: R.77, F.78, V.79, I.131, E.181 Chain E: F.42, R.105 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.131 Hydrogen bonds: A:E.181 Salt bridges: A:R.77, E:R.105 ACT.9: 5 residues within 4Å: Chain A: I.73, P.74, E.75, I.76, R.85 No protein-ligand interaction detected (PLIP) ACT.10: 7 residues within 4Å: Chain A: I.25, F.42, R.105 Chain B: R.77, V.79, I.131, E.181 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.105, B:R.77 Hydrophobic interactions: B:I.131 ACT.17: 8 residues within 4Å: Chain B: L.45, I.73, P.74, E.75, I.76, R.85, Y.102, E.104 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.76 Hydrogen bonds: B:E.104 Salt bridges: B:R.85 ACT.24: 6 residues within 4Å: Chain C: P.74, E.75, I.76, R.85, Y.102, E.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.76 Salt bridges: C:R.85 ACT.25: 5 residues within 4Å: Chain B: F.42, R.105 Chain C: R.77, I.131, E.181 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.131, B:F.42 Salt bridges: C:R.77, B:R.105 ACT.32: 7 residues within 4Å: Chain D: L.45, I.73, P.74, E.75, 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.33: 6 residues within 4Å: Chain C: F.42, R.105 Chain D: R.77, V.79, I.131, E.181 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.131 Salt bridges: D:R.77, C:R.105 ACT.34: 6 residues within 4Å: Chain D: F.42, R.105 Chain E: R.77, V.79, I.131, E.181 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:V.79, E:I.131 Hydrogen bonds: E:E.181 Salt bridges: E:R.77, D:R.105 ACT.42: 8 residues within 4Å: Chain E: L.45, I.73, P.74, E.75, I.76, R.85, Y.102, E.104 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:I.76, E:I.76 Salt bridges: E:R.85

2 x 6E3: 2,3,5,6-tetramethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione(Covalent)

6E3.7: 10 residues within 4Å: Chain A: V.5, S.6, P.7, W.72, E.75, C.135 Chain E: T.65, V.90, D.91, I.92 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:P.7, E:T.65, E:D.91 6E3.29: 10 residues within 4Å: Chain C: T.65, V.90, D.91, I.92 Chain D: P.7, W.72, E.75, C.135, T.137, I.140 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.7, D:W.72, D:I.140 Water bridges: C:E.67

5 x BR: BROMIDE ION(Non-covalent)

BR.8: 2 residues within 4Å: Chain A: F.78, R.85 Ligand excluded by PLIP BR.15: 3 residues within 4Å: Chain B: R.77, F.78, R.85 Ligand excluded by PLIP BR.22: 3 residues within 4Å: Chain C: R.77, F.78, R.85 Ligand excluded by PLIP BR.30: 2 residues within 4Å: Chain D: F.78, R.85 Ligand excluded by PLIP BR.40: 2 residues within 4Å: Chain E: F.78, R.85 Ligand excluded by PLIP

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

NA.16: 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.23: 4 residues within 4Å: Chain C: P.68, E.69, I.71, I.73 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.68, C:I.73 NA.31: 5 residues within 4Å: Chain D: V.5, P.68, I.71, W.72, I.73 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.71, D:I.73 NA.41: 4 residues within 4Å: Chain E: V.5, P.68, I.71, I.73 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:P.68, E:I.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Menny, A. et al., Identification of a pre-active conformation of a pentameric channel receptor. Elife (2017)

Release Date

2017-03-29

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