SMTL ID : 8fe1.1

Alpha1/BetaB Heteromeric Glycine Receptor in 1 mM Glycine 20 uM Ivermectin State

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

5 x GLY: GLYCINE(Non-covalent)

GLY.1: 6 residues within 4Å: Chain A: F.183, T.228, F.231 Chain E: R.189, L.242, S.254 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.254, A:F.183, A:F.183 Salt bridges: E:R.189 GLY.6: 7 residues within 4Å: Chain A: F.87, R.89, L.141, S.153 Chain D: F.183, T.228, F.231 6 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: D:F.183, D:F.183, D:T.228, G.6, A:S.153 Salt bridges: A:R.89 GLY.17: 8 residues within 4Å: Chain B: F.87, R.89, L.141, S.153 Chain E: F.284, Y.327, T.330, Y.333 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: E:F.284, E:T.330, B:S.153, G.17 Salt bridges: B:R.89 GLY.23: 5 residues within 4Å: Chain B: F.183, T.228 Chain C: R.89, L.141, S.153 6 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: C:S.153, B:F.183, B:F.183, B:T.228, G.23 Salt bridges: C:R.89 GLY.25: 6 residues within 4Å: Chain C: F.183, T.228, F.231 Chain D: R.89, L.141, S.153 6 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 3 interactions with chain C Hydrogen bonds: D:S.153, G.25, C:F.183, C:F.183, C:T.228 Salt bridges: D:R.89

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

NAG.2: 4 residues within 4Å: Chain A: N.55, P.59, P.60, N.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.55, A:P.60 NAG.12: 4 residues within 4Å: Chain B: N.55, P.59, P.60, N.62 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.59 Hydrogen bonds: B:P.60, B:N.62 NAG.26: 4 residues within 4Å: Chain C: N.55, P.59, P.60, N.62 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.59 Hydrogen bonds: C:P.60 NAG.37: 3 residues within 4Å: Chain D: P.59, P.60, N.62 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:P.59 Hydrogen bonds: D:P.60 NAG.46: 2 residues within 4Å: Chain E: N.322, T.324 No protein-ligand interaction detected (PLIP) NAG.48: 2 residues within 4Å: Chain E: N.135, D.202 No protein-ligand interaction detected (PLIP)

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.3: 16 residues within 4Å: Chain A: T.288, S.291, R.295, S.302, V.304, D.308, A.312, L.315, L.316, F.319 Chain E: G.347, M.351, A.355, P.356, L.359 Ligands: PLM.52 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:T.288, A:V.304, A:L.315, A:L.316, A:F.319, E:P.356 Hydrogen bonds: A:S.291, A:R.295, A:R.295, E:M.351 IVM.4: 20 residues within 4Å: Chain A: G.245, I.249, Q.250, I.253, P.254, L.256, L.257, I.260 Chain D: T.288, S.291, S.292, S.302, V.304, D.308, A.312, L.315, L.316, F.319 Ligands: PLM.10, PLM.44 14 PLIP interactions: 5 interactions with chain D, 9 interactions with chain A Hydrophobic interactions: D:T.288, D:V.304, D:L.315, D:L.316, D:F.319, A:I.249, A:I.249, A:I.253, A:P.254, A:L.256, A:I.260 Hydrogen bonds: A:I.249, A:Q.250, A:Q.250 IVM.13: 17 residues within 4Å: Chain B: L.248, I.249, Q.250, I.253, P.254, L.256, L.257, I.260 Chain E: S.390, C.393, T.394, V.406, I.414, L.417, L.418 Ligands: PX4.14, PLM.15 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain E Hydrophobic interactions: B:I.249, B:I.253, B:I.253, B:P.254, B:L.256, B:I.260, E:T.394, E:V.406, E:I.414, E:L.417, E:L.418 Hydrogen bonds: B:I.249, B:Q.250 IVM.27: 18 residues within 4Å: Chain B: T.288, S.291, R.295, S.302, V.304, A.312, L.315, L.316, F.319 Chain C: G.245, I.249, Q.250, I.253, P.254, L.257, I.260 Ligands: PX4.16, PLM.31 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:V.304, B:L.315, B:L.316, B:F.319, C:I.249, C:I.253, C:P.254, C:I.260 Hydrogen bonds: B:R.295, C:I.249, C:Q.250 IVM.38: 16 residues within 4Å: Chain C: T.288, S.291, S.302, V.304, D.308, A.312, L.315, L.316, F.319 Chain D: G.245, I.249, Q.250, I.253, P.254, L.257 Ligands: PX4.39 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:V.304, C:L.315, C:L.316, C:F.319, D:I.253, D:P.254 Hydrogen bonds: D:I.249, D:Q.250

8 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PX4.5: 7 residues within 4Å: Chain A: L.248, L.256, W.430, I.431, K.434, R.437 Ligands: PLM.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.248, A:W.430, A:W.430, A:I.431 Salt bridges: A:R.437 PX4.14: 4 residues within 4Å: Chain B: N.426, K.434 Ligands: IVM.13, PLM.15 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.434 PX4.16: 7 residues within 4Å: Chain B: K.167, I.309, V.313, F.425, Y.429, I.436 Ligands: IVM.27 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.313, B:F.425, B:Y.429 Salt bridges: B:K.167 PX4.24: 5 residues within 4Å: Chain B: A.326, A.327, F.330 Chain C: W.267 Ligands: PLM.30 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:W.267, C:W.267, C:W.267, B:A.326, B:A.327, B:F.330, B:F.330, B:F.330 PX4.29: 8 residues within 4Å: Chain C: F.330, R.406 Chain D: I.260, V.264, W.267, R.415 Ligands: PLM.35, PLM.40 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.330, D:I.260, D:V.264, D:W.267, D:W.267 Salt bridges: C:R.406 PX4.36: 8 residues within 4Å: Chain A: W.267 Chain D: L.323, F.330, I.331, Q.334, R.406 Ligands: PLM.9, PLM.42 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.323, D:F.330, D:I.331, A:W.267, A:W.267, A:W.267 Hydrogen bonds: D:Q.334 Salt bridges: D:R.406 PX4.39: 3 residues within 4Å: Chain D: L.248, W.430 Ligands: IVM.38 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.248, D:W.430, D:W.430 PX4.47: 7 residues within 4Å: Chain A: F.330, I.331, R.406 Chain E: L.366, W.369 Ligands: PLM.7, PLM.51 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:F.330, A:F.330, A:I.331, E:L.366, E:W.369, E:W.369, E:W.369 Hydrogen bonds: A:R.406

28 x PLM: PALMITIC ACID(Non-covalent)(Non-functional Binders)

PLM.7: 3 residues within 4Å: Chain A: L.323 Ligands: PLM.11, PX4.47 Ligand excluded by PLIP PLM.8: 3 residues within 4Å: Chain A: K.167, Y.433, I.436 Ligand excluded by PLIP PLM.9: 2 residues within 4Å: Chain A: P.419 Ligands: PX4.36 Ligand excluded by PLIP PLM.10: 2 residues within 4Å: Ligands: IVM.4, PX4.5 Ligand excluded by PLIP PLM.11: 4 residues within 4Å: Chain A: L.316, I.410, V.413 Ligands: PLM.7 Ligand excluded by PLIP PLM.15: 7 residues within 4Å: Chain B: M.171, W.430, Y.433, K.434, R.437 Ligands: IVM.13, PX4.14 Ligand excluded by PLIP PLM.18: 2 residues within 4Å: Chain B: W.267 Chain E: V.429 Ligand excluded by PLIP PLM.19: 1 residues within 4Å: Chain B: V.416 Ligand excluded by PLIP PLM.20: 2 residues within 4Å: Chain B: V.416, L.420 Ligand excluded by PLIP PLM.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PLM.22: 4 residues within 4Å: Chain B: L.316, F.317, R.409, F.418 Ligand excluded by PLIP PLM.30: 2 residues within 4Å: Chain C: P.419 Ligands: PX4.24 Ligand excluded by PLIP PLM.31: 2 residues within 4Å: Ligands: IVM.27, D10.28 Ligand excluded by PLIP PLM.32: 3 residues within 4Å: Chain C: V.304, V.313 Ligands: PLM.33 Ligand excluded by PLIP PLM.33: 6 residues within 4Å: Chain C: K.167, I.309, F.425, F.428, T.432 Ligands: PLM.32 Ligand excluded by PLIP PLM.34: 6 residues within 4Å: Chain C: L.316, F.317, R.409, I.410, V.413 Ligands: PLM.35 Ligand excluded by PLIP PLM.35: 3 residues within 4Å: Chain C: R.406 Ligands: PX4.29, PLM.34 Ligand excluded by PLIP PLM.40: 4 residues within 4Å: Chain D: I.260, V.416 Ligands: PX4.29, PLM.41 Ligand excluded by PLIP PLM.41: 1 residues within 4Å: Ligands: PLM.40 Ligand excluded by PLIP PLM.42: 3 residues within 4Å: Chain D: R.406 Ligands: PX4.36, PLM.45 Ligand excluded by PLIP PLM.43: 1 residues within 4Å: Chain D: Y.433 Ligand excluded by PLIP PLM.44: 2 residues within 4Å: Chain D: I.309 Ligands: IVM.4 Ligand excluded by PLIP PLM.45: 4 residues within 4Å: Chain D: L.316, I.410, V.413 Ligands: PLM.42 Ligand excluded by PLIP PLM.49: 1 residues within 4Å: Chain E: I.411 Ligand excluded by PLIP PLM.50: 3 residues within 4Å: Chain E: A.422, V.429 Ligands: PLM.53 Ligand excluded by PLIP PLM.51: 1 residues within 4Å: Ligands: PX4.47 Ligand excluded by PLIP PLM.52: 3 residues within 4Å: Chain E: V.346, G.347 Ligands: IVM.3 Ligand excluded by PLIP PLM.53: 4 residues within 4Å: Chain E: Y.554, F.559, S.562 Ligands: PLM.50 Ligand excluded by PLIP

1 x D10: DECANE(Non-covalent)

D10.28: 4 residues within 4Å: Chain C: L.248, Y.252, W.430 Ligands: PLM.31 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.248, C:Y.252, C:W.430

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gibbs, E. et al., Conformational transitions and allosteric modulation in a heteromeric glycine receptor. Nat Commun (2023)

Release Date

2023-03-22

Peptides

Glycine receptor subunit alphaZ1: ABCD
Glycine receptor beta subunit 2: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
C

D
B

E
E

Membrane

We predict this structure to be a membrane protein.
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Glycine receptor subunit alphaZ1

Glycine receptor beta subunit 2

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