SMTL ID : 6hjx.1

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) 7'C pore mutant (L238C) in complex with nanobody 72

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-1-1-5-mer

Ligands

4 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.1: 7 residues within 4Å: Chain A: A.1, T.36, G.37, K.38, W.64, Q.130, Q.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.38 P6G.5: 8 residues within 4Å: Chain B: A.4, V.7, T.39, G.40, K.41, W.67, Q.133, Q.134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.41 P6G.10: 9 residues within 4Å: Chain D: A.1, R.2, V.4, T.36, G.37, W.64, Y.127, Q.130, Q.131 No protein-ligand interaction detected (PLIP) P6G.12: 7 residues within 4Å: Chain E: R.3, T.37, G.38, K.39, W.65, Q.131, Q.132 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.2

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.2: 12 residues within 4Å: Chain A: A.209, S.213, W.216, R.293, L.294, P.297 Chain B: F.269, L.273, I.276, H.280, R.281, A.283 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.269, B:L.273, B:I.276, B:I.276, A:L.294, A:P.297

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

LMT.3: 6 residues within 4Å: Chain A: T.251, Q.256, I.259, G.263 Chain E: S.195, W.199 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.259 Hydrogen bonds: A:T.251, A:T.251, A:Q.256 LMT.4: 9 residues within 4Å: Chain A: W.198 Chain B: T.254, Q.259, I.262, S.267, A.270, F.299, F.303, I.306 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.262, B:A.270, B:F.299, B:F.303, B:I.306 Hydrogen bonds: B:T.254, B:T.254, A:W.198 LMT.6: 9 residues within 4Å: Chain B: W.201 Chain C: R.112, T.254, Q.259, I.262, A.263, F.303, I.306, L.310 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.262, C:F.303, C:I.306, C:L.310, C:L.310 Hydrogen bonds: C:R.112, C:T.254, C:T.254, B:W.201 LMT.9: 7 residues within 4Å: Chain C: S.197, W.201 Chain D: T.251, Q.256, I.259, A.260, L.307 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.259, D:L.307 Hydrogen bonds: D:T.251, D:T.251, C:S.197, C:S.197, C:W.201 LMT.11: 7 residues within 4Å: Chain D: W.198 Chain E: T.252, Q.257, A.261, G.264, S.265, F.301 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:Q.257, E:A.261, E:F.301 Hydrogen bonds: E:T.252, E:T.252, E:Q.257, D:W.198

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 3 residues within 4Å: Chain B: K.49 Chain C: Q.134, Q.180 No protein-ligand interaction detected (PLIP)

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

NA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henault, C.M. et al., A lipid site shapes the agonist response of a pentameric ligand-gated ion channel. Nat.Chem.Biol. (2019)

Release Date

2019-10-09

Peptides

Cys-loop ligand-gated ion channel: A
Cys-loop ligand-gated ion channel: B
Cys-loop ligand-gated ion channel: C
Cys-loop ligand-gated ion channel: D
Cys-loop ligand-gated ion channel: E
nanobody 72: FGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Membrane

We predict this structure to be a membrane protein.
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Cys-loop ligand-gated ion channel

Cys-loop ligand-gated ion channel

Cys-loop ligand-gated ion channel

Cys-loop ligand-gated ion channel

Cys-loop ligand-gated ion channel

nanobody 72

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