SMTL ID : 6vm0.1

Full length Glycine receptor reconstituted in lipid nanodisc in Gly/IVM-conformation (State-1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 4 residues within 4Å: Chain A: P.59, P.60, N.62, I.191 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: P.59, P.60, N.62, I.191 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: P.59, P.60, N.62, I.191 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: P.59, P.60, N.62, I.191 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain E: P.59, P.60, N.62, I.191 No protein-ligand interaction detected (PLIP)

5 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.6: 6 residues within 4Å: Chain A: L.316, F.317, S.320, V.413, F.418, V.421 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.316, A:F.317, A:F.418, A:V.421 PIO.10: 6 residues within 4Å: Chain B: L.316, F.317, S.320, V.413, F.418, V.421 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.316, B:F.317, B:F.418, B:V.421 PIO.12: 6 residues within 4Å: Chain C: L.316, F.317, S.320, V.413, F.418, V.421 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.316, C:F.317, C:F.418, C:V.421 PIO.17: 6 residues within 4Å: Chain D: L.316, F.317, S.320, V.413, F.418, V.421 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.316, D:F.317, D:F.418, D:V.421 PIO.20: 6 residues within 4Å: Chain E: L.316, F.317, S.320, V.413, F.418, V.421 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.316, E:F.317, E:F.418, E:V.421

5 x GLY: GLYCINE(Non-covalent)

GLY.7: 8 residues within 4Å: Chain A: F.87, R.89, L.141, S.153 Chain B: F.183, Y.226, T.228, F.231 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:T.228, A:S.153, G.7, G.7 Salt bridges: A:R.89 GLY.11: 8 residues within 4Å: Chain B: F.87, R.89, L.141, S.153 Chain E: F.183, Y.226, T.228, F.231 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: E:T.228, B:S.153, G.11, G.11 Salt bridges: B:R.89 GLY.13: 8 residues within 4Å: Chain C: F.87, R.89, L.141, S.153 Chain D: F.183, Y.226, T.228, F.231 5 PLIP interactions: 2 interactions with chain C, 2 Ligand-Ligand interactions, 1 interactions with chain D Hydrogen bonds: C:S.153, G.13, G.13, D:T.228 Salt bridges: C:R.89 GLY.15: 8 residues within 4Å: Chain A: F.183, Y.226, T.228, F.231 Chain D: F.87, R.89, L.141, S.153 5 PLIP interactions: 2 interactions with chain D, 2 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: D:S.153, G.15, G.15, A:T.228 Salt bridges: D:R.89 GLY.19: 8 residues within 4Å: Chain C: F.183, Y.226, T.228, F.231 Chain E: F.87, R.89, L.141, S.153 5 PLIP interactions: 2 interactions with chain E, 2 Ligand-Ligand interactions, 1 interactions with chain C Hydrogen bonds: E:S.153, G.19, G.19, C:T.228 Salt bridges: E:R.89

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.8: 14 residues within 4Å: Chain A: T.288, S.291, S.292, R.295, S.302, V.304, D.308, A.312, L.315 Chain D: I.249, I.253, P.254, L.257, I.260 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:I.249, D:I.253, D:P.254, D:L.257, D:I.260, A:L.315, A:L.315 Hydrogen bonds: D:I.249, A:S.291, A:R.295 IVM.9: 14 residues within 4Å: Chain A: I.249, I.253, P.254, L.257, I.260 Chain B: T.288, S.291, S.292, R.295, S.302, V.304, D.308, A.312, L.315 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.249, A:I.253, A:P.254, A:L.257, A:I.260, B:L.315 Hydrogen bonds: A:I.249, B:S.291, B:R.295 IVM.14: 14 residues within 4Å: Chain C: T.288, S.291, S.292, R.295, S.302, V.304, D.308, A.312, L.315 Chain E: I.249, I.253, P.254, L.257, I.260 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain E Hydrophobic interactions: C:L.315, C:L.315, E:I.249, E:I.253, E:P.254, E:L.257, E:I.260 Hydrogen bonds: C:S.291, C:R.295, E:I.249 IVM.16: 15 residues within 4Å: Chain C: I.249, I.253, P.254, L.257, I.260 Chain D: T.288, S.291, S.292, R.295, S.302, V.304, D.308, A.312, L.315, L.316 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:L.315, D:L.315, D:L.316, C:I.249, C:I.253, C:P.254, C:L.257, C:I.260 Hydrogen bonds: D:S.291, D:R.295, C:I.249 IVM.18: 14 residues within 4Å: Chain B: I.249, I.253, P.254, L.257, I.260 Chain E: T.288, S.291, S.292, R.295, S.302, V.304, D.308, A.312, L.315 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain E Hydrophobic interactions: B:I.249, B:I.253, B:P.254, B:L.257, B:I.260, E:L.315, E:L.315 Hydrogen bonds: B:I.249, E:S.291, E:R.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs. Nat Commun (2020)

Release Date

2020-07-29

Peptides

Glycine receptor subunit alphaZ1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
C

D
B

E
D

Membrane

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

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