SMTL ID : 3rhw.1

C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab and ivermectin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.26 Å

Oligo State

hetero-5-5-5-mer

Ligands

5 x IVM: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside(Non-covalent)

IVM.1: 17 residues within 4Å: Chain A: L.217, L.218, Q.219, I.222, P.223, M.226 Chain E: T.257, S.260, I.273, D.277, I.280, G.281, M.284, T.285, F.288 Ligands: LMT.3, OCT.16 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:I.222, A:P.223, A:M.226, E:T.257, E:M.284, E:F.288, E:F.288 Hydrogen bonds: A:L.218, E:S.260, E:S.260 IVM.5: 15 residues within 4Å: Chain A: T.257, S.260, I.273, D.277, I.280, G.281, M.284, T.285, F.288 Chain B: L.217, L.218, Q.219, I.222, P.223, M.226 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.222, B:P.223, B:M.226, A:T.257, A:M.284, A:F.288 Hydrogen bonds: B:L.218, A:S.260, A:S.260 IVM.6: 15 residues within 4Å: Chain B: T.257, S.260, I.273, D.277, I.280, G.281, M.284, T.285, F.288 Chain C: L.217, L.218, Q.219, I.222, P.223, M.226 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:T.257, B:M.284, B:F.288, B:F.288, C:I.222, C:P.223, C:M.226 Hydrogen bonds: B:S.260, B:S.260, C:L.218 IVM.12: 15 residues within 4Å: Chain C: T.257, S.260, I.273, D.277, I.280, G.281, M.284, T.285, F.288 Chain D: L.217, L.218, Q.219, I.222, P.223, M.226 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:T.257, C:M.284, C:F.288, C:F.288, D:P.223, D:M.226 Hydrogen bonds: C:S.260, C:S.260, D:L.218 IVM.13: 16 residues within 4Å: Chain D: T.257, S.260, I.273, D.277, I.280, G.281, M.284, T.285, F.288 Chain E: L.217, L.218, Q.219, I.222, P.223, M.226 Ligands: OCT.14 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:T.257, D:F.288, D:F.288, E:I.222, E:P.223, E:M.226 Hydrogen bonds: D:S.260, D:S.260, E:L.218

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

LMT.2: 8 residues within 4Å: Chain A: H.299, I.300, N.302, A.303, G.304, T.305, W.308 Ligands: LMT.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.300 Hydrogen bonds: A:N.302, A:G.304, A:T.305 Salt bridges: A:H.299 LMT.3: 3 residues within 4Å: Chain A: K.210, W.335 Ligands: IVM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.210, A:K.210 LMT.7: 5 residues within 4Å: Chain B: W.236, L.317, R.320 Ligands: LMT.2, UND.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.320

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 6 residues within 4Å: Chain B: Q.143, N.185, T.186, S.187, T.206, Q.208 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.206 Hydrogen bonds: B:Q.143 NAG.10: 7 residues within 4Å: Chain C: Q.143, N.185, T.186, S.187, T.206, I.207, Q.208 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Q.143, C:T.206, C:Q.208 Hydrogen bonds: C:Q.208 NAG.15: 6 residues within 4Å: Chain E: Q.143, N.185, T.186, S.187, T.206, Q.208 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.206 Hydrogen bonds: E:Q.143

3 x OCT: N-OCTANE(Non-covalent)

OCT.8: 5 residues within 4Å: Chain B: A.282, T.285, F.286, C.289, F.323 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.282, B:T.285, B:F.286, B:F.286, B:F.323 OCT.14: 3 residues within 4Å: Chain D: T.285, F.286 Ligands: IVM.13 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.285, D:F.286, D:F.286 OCT.16: 4 residues within 4Å: Chain E: A.282, T.285, F.286 Ligands: IVM.1 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:A.282, E:T.285

1 x UND: UNDECANE(Non-covalent)

UND.9: 4 residues within 4Å: Chain B: W.236, R.320, P.324 Ligands: LMT.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.236, B:P.324

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hibbs, R.E. et al., Principles of activation and permeation in an anion-selective Cys-loop receptor. Nature (2011)

Release Date

2011-05-25

Peptides

Avermectin-sensitive glutamate-gated chloride channel GluCl alpha: ABCDE
Mouse monoclonal Fab fragment, heavy chain: FGHIJ
Mouse monoclonal Fab fragment, light chain: KLMNO

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

K
K

L
L

M
M

N
N

O
O

Membrane

We predict this structure to be a membrane protein.
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Avermectin-sensitive glutamate-gated chloride channel GluCl alpha

Mouse monoclonal Fab fragment, heavy chain

Mouse monoclonal Fab fragment, light chain

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