SMTL ID : 3p50.1

Structure of propofol bound to a pentameric ligand-gated ion channel, GLIC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-pentamer

Ligands

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

LMT.1: 4 residues within 4Å: Chain A: A.237, I.240 Chain E: A.237 Ligands: LMT.2 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:A.237, A:A.237, A:I.240, A:I.240 LMT.2: 16 residues within 4Å: Chain A: T.226, S.230, I.233 Chain B: T.226, S.230, I.233 Chain C: T.226, S.230, I.233 Chain D: S.230, I.233 Ligands: LMT.1, LMT.6, LMT.13, LMT.14, LMT.18 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:S.230, A:S.230, C:S.230, B:T.226 LMT.6: 8 residues within 4Å: Chain A: A.237 Chain B: I.233, A.237, I.240, L.241 Chain C: T.244 Ligands: LMT.2, LMT.13 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.233, B:A.237, B:I.240, B:L.241, A:A.237 LMT.13: 6 residues within 4Å: Chain B: A.237 Chain C: A.237, I.240 Chain D: T.244 Ligands: LMT.2, LMT.6 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:A.237, C:I.240, D:T.244, B:A.237 LMT.14: 6 residues within 4Å: Chain C: A.237 Chain D: A.237, I.240, T.244 Chain E: T.244 Ligands: LMT.2 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.237, D:I.240, C:A.237 LMT.18: 4 residues within 4Å: Chain A: T.244 Chain E: A.237, I.240 Ligands: LMT.2 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:A.237, E:I.240

5 x PFL: 2,6-BIS(1-METHYLETHYL)PHENOL(Non-covalent)

PFL.3: 8 residues within 4Å: Chain A: P.120, I.202, L.206, Y.254, T.255, I.258, N.307 Ligands: PLC.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.202, A:I.202, A:L.206, A:Y.254, A:T.255, A:I.258 Hydrogen bonds: A:Y.254, A:Y.254 PFL.7: 8 residues within 4Å: Chain B: P.120, I.202, L.206, Y.254, T.255, I.258, N.307 Ligands: PLC.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.202, B:I.202, B:L.206, B:Y.254, B:T.255, B:I.258 Hydrogen bonds: B:Y.254, B:Y.254 PFL.10: 8 residues within 4Å: Chain C: P.120, I.202, L.206, Y.254, T.255, I.258, N.307 Ligands: PLC.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.202, C:I.202, C:L.206, C:Y.254, C:T.255, C:I.258 Hydrogen bonds: C:Y.254, C:Y.254 PFL.15: 9 residues within 4Å: Chain D: P.120, I.202, L.206, Y.254, T.255, I.258, N.307 Ligands: PLC.16, PLC.17 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.202, D:I.202, D:L.206, D:Y.254, D:T.255, D:I.258 Hydrogen bonds: D:Y.254, D:Y.254 PFL.19: 8 residues within 4Å: Chain E: P.120, I.202, L.206, Y.254, T.255, I.258, N.307 Ligands: PLC.20 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.202, E:I.202, E:L.206, E:Y.254, E:T.255, E:I.258 Hydrogen bonds: E:Y.254

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

PLC.4: 6 residues within 4Å: Chain A: R.118, F.121, Y.194, F.315 Ligands: PFL.3, PLC.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.121, A:Y.194 Hydrogen bonds: A:F.121 PLC.5: 1 residues within 4Å: Ligands: PLC.4 No protein-ligand interaction detected (PLIP) PLC.8: 6 residues within 4Å: Chain B: R.118, F.121, Y.194, F.315 Ligands: PFL.7, PLC.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.121, B:Y.194 Hydrogen bonds: B:F.121 PLC.9: 1 residues within 4Å: Ligands: PLC.8 No protein-ligand interaction detected (PLIP) PLC.11: 6 residues within 4Å: Chain C: R.118, F.121, Y.194, F.315 Ligands: PFL.10, PLC.12 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.121, C:Y.194 Hydrogen bonds: C:F.121 PLC.12: 1 residues within 4Å: Ligands: PLC.11 No protein-ligand interaction detected (PLIP) PLC.16: 6 residues within 4Å: Chain D: R.118, F.121, Y.194, F.315 Ligands: PFL.15, PLC.17 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.121, D:Y.194 Hydrogen bonds: D:F.121 PLC.17: 5 residues within 4Å: Chain D: L.304, N.307, A.311 Ligands: PFL.15, PLC.16 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.304, D:N.307 PLC.20: 6 residues within 4Å: Chain E: R.118, F.121, Y.194, F.315 Ligands: PFL.19, PLC.21 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.121, E:Y.194 Hydrogen bonds: E:F.121 PLC.21: 1 residues within 4Å: Ligands: PLC.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nury, H. et al., X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Nature (2011)

Release Date

2011-01-19

Peptides

Glr4197 protein: 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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Glr4197 protein

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