SMTL ID : 6ssi.1

Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-5-5-mer

Ligands

5 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.1: 9 residues within 4Å: Chain A: E.127, P.128, F.129, Y.171, H.173, L.174, F.184 Chain B: R.87 Ligands: GOL.7 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.87 Hydrophobic interactions: A:Y.171, A:F.184 Hydrogen bonds: A:F.129, A:F.129 ABU.5: 10 residues within 4Å: Chain B: E.127, P.128, F.129, Y.171, H.173, L.174, F.184 Chain C: R.87, N.99 Ligands: GOL.14 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.184 Hydrogen bonds: B:E.127, B:E.127, C:N.99 Salt bridges: B:H.173, C:R.87 ABU.12: 9 residues within 4Å: Chain C: E.127, P.128, F.129, Y.171, H.173, L.174, F.184 Chain D: R.87 Ligands: GOL.20 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Salt bridges: D:R.87 Hydrophobic interactions: C:Y.171, C:F.184 Hydrogen bonds: C:E.127, C:F.129, C:H.173 ABU.18: 9 residues within 4Å: Chain D: E.127, P.128, F.129, Y.171, H.173, L.174, F.184 Chain E: R.87 Ligands: GOL.26 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:Y.171, D:F.184 Hydrogen bonds: D:E.127, D:F.129 Salt bridges: D:H.173, E:R.87 ABU.24: 10 residues within 4Å: Chain A: R.87, N.99 Chain E: E.127, P.128, F.129, Y.171, H.173, F.184 Ligands: GOL.3, GOL.27 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:N.99, E:E.127 Water bridges: A:R.87, A:R.87 Salt bridges: A:R.87, E:H.173 Hydrophobic interactions: E:F.184

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

MES.2: 4 residues within 4Å: Chain A: G.41, K.42, W.68, Y.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.42 Water bridges: A:W.68 pi-Cation interactions: A:W.68, A:W.68 MES.6: 3 residues within 4Å: Chain B: G.41, W.68, Y.131 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.42 Water bridges: B:W.68 pi-Cation interactions: B:W.68, B:W.68 MES.13: 3 residues within 4Å: Chain C: G.41, W.68, Y.131 4 PLIP interactions: 4 interactions with chain C Water bridges: C:W.68, C:W.68 pi-Cation interactions: C:W.68, C:W.68 MES.19: 4 residues within 4Å: Chain D: G.41, K.42, W.68, Y.131 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.42 Water bridges: D:W.68 Salt bridges: D:K.42 pi-Cation interactions: D:W.68, D:W.68 MES.25: 4 residues within 4Å: Chain E: G.41, K.42, W.68, Y.131 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.42 Water bridges: E:W.68, E:W.68 pi-Cation interactions: E:W.68, E:W.68

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: F.15, Y.34, V.36, N.99 Chain E: Y.171, H.173 Ligands: ABU.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.99, A:N.99 GOL.7: 8 residues within 4Å: Chain A: F.129, H.173 Chain B: F.15, Y.34, V.36, R.87, N.99 Ligands: ABU.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.87, B:N.99, A:F.129 GOL.14: 7 residues within 4Å: Chain B: Y.171, H.173 Chain C: F.15, Y.34, V.36, N.99 Ligands: ABU.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.87, C:N.99 GOL.20: 6 residues within 4Å: Chain C: Y.171, H.173 Chain D: F.15, Y.34, N.99 Ligands: ABU.12 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:H.173, D:N.99, D:N.99 GOL.26: 7 residues within 4Å: Chain D: Y.171, H.173 Chain E: F.15, Y.34, V.36, N.99 Ligands: ABU.18 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.99, E:N.99 GOL.27: 8 residues within 4Å: Chain A: R.87, M.89 Chain E: S.130, N.132, L.174, Q.181, F.184 Ligands: ABU.24 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:N.132, E:Q.181, A:R.87 Water bridges: A:R.87

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: D.149, E.151, D.154 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.149, A:E.151, A:D.154, A:D.154 CA.9: 4 residues within 4Å: Chain A: D.109 Chain B: D.149, E.151, D.154 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.149, B:D.154 CA.16: 3 residues within 4Å: Chain C: D.149, E.151, D.154 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.149, C:E.151, C:D.154, C:D.154 CA.22: 3 residues within 4Å: Chain D: D.149, E.151, D.154 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.149, D:E.151, D:D.154, D:D.154 CA.29: 4 residues within 4Å: Chain D: D.109 Chain E: D.149, E.151, D.154 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Metal complexes: E:E.151, E:D.154, E:D.154, D:D.109

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 12 residues within 4Å: Chain B: I.35, I.59, V.69, P.70, A.71, L.72, F.74, T.83, K.86, Y.98, A.100, F.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.72 PG4.15: 8 residues within 4Å: Chain C: I.75, S.107, N.108, E.125, I.169, R.170, R.186 Chain D: N.147 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.108, C:R.170, C:R.186 PG4.21: 10 residues within 4Å: Chain D: I.35, I.59, I.63, V.69, P.70, A.71, L.72, K.86, Y.98, A.100 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.83, D:K.86, D:Y.98 Water bridges: D:E.60 PG4.28: 10 residues within 4Å: Chain E: I.35, I.59, I.63, V.69, P.70, A.71, L.72, K.86, Y.98, A.100 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.72, E:K.86

5 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.10: 10 residues within 4Å: Chain A: T.255, Q.260, I.263, A.264, G.267, S.268, I.307 Chain B: E.152, S.198, W.202 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.152, B:W.202, A:T.255, A:T.255 Hydrophobic interactions: A:I.263, A:I.307, A:I.307 UMQ.11: 9 residues within 4Å: Chain B: R.113, T.255, Q.260, I.263, A.264, S.268, F.304 Chain C: E.152, W.202 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.263, B:A.264, B:F.304 Hydrogen bonds: B:R.113, B:T.255, B:Q.260, C:W.202 UMQ.17: 9 residues within 4Å: Chain C: T.255, Q.260, I.263, A.264, S.268, F.304, I.307 Chain D: S.198, W.202 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.263, C:A.264, C:F.304, C:I.307, C:I.307 Hydrogen bonds: C:T.255, D:S.198 UMQ.31: 7 residues within 4Å: Chain A: S.198, W.202 Chain E: T.255, Q.260, I.263, A.264, I.307 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:I.263, E:I.307, E:I.307 Hydrogen bonds: E:T.255, E:T.255, A:W.202 UMQ.32: 9 residues within 4Å: Chain D: T.255, Q.260, I.263, A.264, G.267, I.307 Chain E: E.152, S.198, W.202 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.263, D:I.307 Hydrogen bonds: D:T.255, D:Q.260

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

ACT.23: 4 residues within 4Å: Chain C: S.80 Chain D: D.82, T.83, G.84 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.80 ACT.30: 4 residues within 4Å: Chain D: S.80 Chain E: D.82, T.83, G.84 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brams, M. et al., Modulation of the Erwinia ligand-gated ion channel (ELIC) and the 5-HT 3 receptor via a common vestibule site. Elife (2020)

Release Date

2020-02-12

Peptides

Cys-loop ligand-gated ion channel: ABCDE
NANOBODY 22: 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

NANOBODY 22

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