SMTL ID : 4f8h.1

X-ray Structure of the Anesthetic Ketamine Bound to the GLIC Pentameric Ligand-gated Ion Channel

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

homo-pentamer

Ligands

5 x RKE: (R)-ketamine(Non-covalent)

RKE.1: 8 residues within 4Å: Chain A: Y.23, N.152, D.153, D.154 Chain B: V.79, F.174, L.176, K.183 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.79, B:F.174, B:F.174, B:F.174, B:F.174, B:F.174, B:L.176, A:Y.23, A:N.152 Halogen bonds: B:K.183 Hydrogen bonds: A:Y.23, A:D.153, A:D.154 RKE.5: 8 residues within 4Å: Chain B: Y.23, N.152, D.153, D.154 Chain C: V.79, F.174, L.176, K.183 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:Y.23, B:N.152, C:V.79, C:F.174, C:F.174, C:F.174, C:F.174, C:L.176 Hydrogen bonds: B:Y.23, B:D.153, B:D.154 Halogen bonds: C:K.183 RKE.9: 8 residues within 4Å: Chain C: Y.23, N.152, D.153, D.154 Chain D: V.79, F.174, L.176, K.183 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.79, D:F.174, D:F.174, D:F.174, D:L.176, C:Y.23, C:N.152 Halogen bonds: D:K.183 Hydrogen bonds: C:Y.23, C:D.153, C:D.154 RKE.14: 8 residues within 4Å: Chain D: Y.23, N.152, D.153, D.154 Chain E: V.79, F.174, L.176, K.183 13 PLIP interactions: 8 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:V.79, E:F.174, E:F.174, E:F.174, E:F.174, E:F.174, E:L.176, D:Y.23, D:N.152 Halogen bonds: E:K.183 Hydrogen bonds: D:Y.23, D:D.153, D:D.154 RKE.18: 8 residues within 4Å: Chain A: V.79, F.174, L.176, K.183 Chain E: Y.23, N.152, D.153, D.154 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:V.79, A:F.174, A:F.174, A:F.174, A:F.174, A:L.176, E:Y.23, E:N.152 Halogen bonds: A:K.183 Hydrogen bonds: E:Y.23, E:D.153, E:D.154

6 x LMD: tetradecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside(Non-covalent)

LMD.2: 16 residues within 4Å: Chain A: D.31, K.33, I.233, A.237, I.240, L.241, T.244, N.245 Chain B: K.33, T.244 Chain E: I.233, A.234, A.237 Ligands: LMD.6, LMD.13, LMD.19 10 PLIP interactions: 6 interactions with chain A, 3 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: A:I.240, A:L.241, E:I.233, E:A.234, E:A.237 Hydrogen bonds: A:D.31, A:T.244, A:T.244, A:T.244 Salt bridges: B:K.33 LMD.6: 16 residues within 4Å: Chain A: I.233, A.234, A.237 Chain B: D.31, K.33, I.233, A.237, I.240, L.241, T.244, N.245 Chain C: K.33, T.244 Ligands: LMD.2, LMD.10, LMD.13 10 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:I.233, B:A.237, B:L.241, A:A.237 Hydrogen bonds: B:T.244, B:T.244, B:T.244, B:N.245 Water bridges: B:D.32 Salt bridges: C:K.33 LMD.10: 15 residues within 4Å: Chain B: I.233, A.234, A.237 Chain C: D.31, I.233, I.236, A.237, I.240, T.244, N.245 Chain D: K.33, T.244 Ligands: LMD.6, LMD.13, LMD.15 8 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C, 2 interactions with chain B Salt bridges: D:K.33 Hydrophobic interactions: C:I.236, C:A.237, B:I.233, B:A.237 Hydrogen bonds: C:T.244, C:T.244, C:N.245 LMD.13: 14 residues within 4Å: Chain A: I.233 Chain B: S.230, I.233 Chain C: S.230, I.233 Chain D: S.230, I.233 Chain E: S.230, I.233 Ligands: LMD.2, LMD.6, LMD.10, LMD.15, LMD.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.230, B:S.230 LMD.15: 15 residues within 4Å: Chain C: A.234, A.237 Chain D: D.31, I.233, I.236, A.237, I.240, L.241, T.244, N.245 Chain E: K.33, T.244 Ligands: LMD.10, LMD.13, LMD.19 12 PLIP interactions: 9 interactions with chain D, 1 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: D:I.233, D:I.236, D:A.237, D:I.240, D:I.240, D:L.241, C:A.234, C:A.237 Hydrogen bonds: D:D.31, D:T.244, D:T.244 Salt bridges: E:K.33 LMD.19: 15 residues within 4Å: Chain A: K.33, T.244 Chain D: I.233, A.237 Chain E: D.31, I.233, I.236, A.237, I.240, L.241, T.244, N.245 Ligands: LMD.2, LMD.13, LMD.15 12 PLIP interactions: 8 interactions with chain E, 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: E:I.233, E:I.236, E:A.237, E:L.241, A:T.244, D:A.237 Hydrogen bonds: E:D.31, E:T.244, E:T.244, E:T.244, A:T.244 Salt bridges: A:K.33

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

PC1.3: 9 residues within 4Å: Chain A: R.118, F.121, Y.194, I.198, L.203, Y.254, I.258, N.307, F.315 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.121, A:F.121, A:F.121, A:Y.194, A:I.198, A:L.203, A:Y.254, A:I.258 Hydrogen bonds: A:R.118 PC1.4: 9 residues within 4Å: Chain A: R.117, R.118, Y.251, M.252, A.257, F.260, M.261, L.313, F.314 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.251, A:M.252, A:A.257, A:F.260 Salt bridges: A:R.117 PC1.7: 10 residues within 4Å: Chain B: R.118, F.121, Y.194, I.198, I.202, L.203, Y.254, N.307, F.315 Ligands: PC1.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.121, B:F.121, B:Y.194, B:Y.194, B:I.202, B:L.203 Hydrogen bonds: B:R.118 PC1.8: 4 residues within 4Å: Chain B: R.118, L.313, F.314 Ligands: PC1.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.314 PC1.11: 10 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 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.121, C:Y.194, C:Y.194, C:I.198, C:I.202, C:L.206, C:Y.254, C:I.258 Hydrogen bonds: C:R.118 PC1.12: 7 residues within 4Å: Chain B: F.195 Chain C: Y.251, M.252, M.261, L.264, L.313, F.314 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.195, C:M.261, C:L.264 Hydrogen bonds: C:M.252 PC1.16: 8 residues within 4Å: Chain D: R.118, F.121, Y.194, I.198, L.203, Y.254, N.307, F.315 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.194, D:Y.194, D:L.203, D:Y.254 Salt bridges: D:R.118 PC1.17: 7 residues within 4Å: Chain C: F.195 Chain D: R.118, M.252, A.257, F.260, L.313, F.314 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:M.252, D:A.257, D:F.260 Hydrogen bonds: D:L.313 PC1.20: 9 residues within 4Å: Chain E: F.121, S.123, E.163, S.191, Y.194, I.198, Y.254, N.307, F.315 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:F.121, E:F.121, E:F.121, E:Y.194, E:Y.194, E:I.198, E:Y.254 Hydrogen bonds: E:S.123 Salt bridges: E:E.163 PC1.21: 9 residues within 4Å: Chain D: I.198 Chain E: R.118, Y.251, M.252, A.257, F.260, M.261, L.313, F.314 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:M.252, E:A.257, E:F.260, E:F.260, E:F.314, D:I.198 Hydrogen bonds: E:M.252, E:L.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, J. et al., Structure of the Pentameric Ligand-Gated Ion Channel GLIC Bound with Anesthetic Ketamine. Structure (2012)

Release Date

2012-08-29

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

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