SMTL ID : 3p4w.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-pentamer

Ligands

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

LMT.1: 5 residues within 4Å: Chain A: I.233, A.237, I.240 Chain E: A.237 Ligands: LMT.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.233, A:A.237, A:I.240, E:A.237 LMT.2: 5 residues within 4Å: Ligands: LMT.1, LMT.6, LMT.10, LMT.11, LMT.18 No protein-ligand interaction detected (PLIP) LMT.6: 6 residues within 4Å: Chain A: A.237 Chain B: I.233, A.237, I.240, L.241 Ligands: LMT.2 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.233, B:I.240, B:L.241, A:A.237 LMT.10: 7 residues within 4Å: Chain B: A.237 Chain C: I.236, A.237, I.240, L.241 Chain D: T.244 Ligands: LMT.2 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: D:T.244, B:A.237, C:I.236, C:A.237, C:L.241 LMT.11: 9 residues within 4Å: Chain C: A.237 Chain D: I.233, I.236, A.237, I.240, L.241, T.244 Chain E: T.244 Ligands: LMT.2 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.233, D:I.236, D:A.237, D:I.240, C:A.237 LMT.18: 3 residues within 4Å: 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 DSF: (2S)-2-(difluoromethoxy)-1,1,1,2-tetrafluoroethane(Non-covalent)

DSF.3: 9 residues within 4Å: Chain A: Y.119, P.120, Y.197, I.201, I.202, V.242, Y.254, T.255, I.258 No protein-ligand interaction detected (PLIP) DSF.7: 12 residues within 4Å: Chain B: Y.119, P.120, Y.197, I.201, I.202, M.205, V.242, Y.254, T.255, I.258, I.259 Ligands: PLC.8 No protein-ligand interaction detected (PLIP) DSF.12: 8 residues within 4Å: Chain C: Y.119, P.120, Y.197, I.201, I.202, V.242, T.255, I.258 No protein-ligand interaction detected (PLIP) DSF.15: 12 residues within 4Å: Chain D: Y.119, P.120, F.121, Y.197, I.201, I.202, M.205, V.242, Y.254, T.255, I.258, I.259 No protein-ligand interaction detected (PLIP) DSF.19: 11 residues within 4Å: Chain E: P.120, F.121, Y.197, I.201, I.202, M.205, V.242, Y.254, T.255, I.258, I.259 No protein-ligand interaction detected (PLIP)

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

PLC.4: 8 residues within 4Å: Chain A: R.118, F.121, Y.194, I.202, L.206, Y.254, N.307, F.315 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.121, A:F.121, A:Y.194, A:I.202, A:L.206, A:Y.254 Hydrogen bonds: A:F.121, A:Y.254 PLC.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PLC.8: 10 residues within 4Å: Chain B: R.118, F.121, Y.194, I.202, L.206, Y.254, N.307, F.315 Ligands: DSF.7, PLC.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.121, B:F.121, B:F.121, B:Y.194, B:I.202, B:L.206, B:Y.254 Hydrogen bonds: B:F.121, B:Y.254 PLC.9: 1 residues within 4Å: Ligands: PLC.8 No protein-ligand interaction detected (PLIP) PLC.13: 8 residues within 4Å: Chain C: R.118, F.121, Y.194, I.202, L.206, Y.254, N.307, F.315 9 PLIP interactions: 9 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 Hydrogen bonds: C:F.121, C:Y.254 PLC.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PLC.16: 9 residues within 4Å: Chain D: R.118, F.121, Y.194, I.202, L.206, Y.254, N.307, F.315 Ligands: PLC.17 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.121, D:F.121, D:F.121, D:Y.194, D:I.202, D:L.206, D:Y.254 Hydrogen bonds: D:F.121, D:Y.254 PLC.17: 1 residues within 4Å: Ligands: PLC.16 No protein-ligand interaction detected (PLIP) PLC.20: 8 residues within 4Å: Chain E: R.118, F.121, Y.194, I.202, L.206, Y.254, N.307, F.315 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.121, E:F.121, E:F.121, E:Y.194, E:I.202, E:L.206, E:Y.254 Hydrogen bonds: E:F.121 PLC.21: 0 residues within 4Å: (No contacts) 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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