SMTL ID : 6vm3.1

Full length Glycine receptor reconstituted in lipid nanodisc in Gly/IVM-conformation (State-3)

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 GLY: GLYCINE(Non-covalent)

GLY.6: 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: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.153, B:T.228, G.6, G.6 Salt bridges: A:R.89 GLY.10: 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: 1 interactions with chain A, 2 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: A:T.228, D:S.153, G.10, G.10 Salt bridges: D:R.89 GLY.11: 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, 1 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: C:S.153, D:T.228, G.11, G.11 Salt bridges: C:R.89 GLY.13: 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.13, G.13, C:T.228 Salt bridges: E:R.89 GLY.14: 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: 2 interactions with chain B, 2 Ligand-Ligand interactions, 1 interactions with chain E Hydrogen bonds: B:S.153, G.14, G.14, E:T.228 Salt bridges: B: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.7: 12 residues within 4Å: Chain A: T.288, S.291, R.295, V.304, A.312, L.315 Chain D: I.249, Q.250, I.253, P.254, L.256, L.257 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:I.253, D:P.254, D:L.256, D:L.257, A:T.288, A:V.304, A:L.315, A:L.315 Hydrogen bonds: D:I.249, D:Q.250, A:S.291, A:R.295 IVM.8: 12 residues within 4Å: Chain A: I.249, Q.250, I.253, P.254, L.256, L.257 Chain B: T.288, S.291, R.295, V.304, A.312, L.315 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:T.288, B:L.315, B:L.315, A:I.253, A:P.254, A:L.256, A:L.257 Hydrogen bonds: B:S.291, B:R.295, A:I.249, A:Q.250 IVM.9: 12 residues within 4Å: Chain C: T.288, S.291, R.295, V.304, A.312, L.315 Chain E: I.249, Q.250, I.253, P.254, L.256, L.257 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain E Hydrophobic interactions: C:T.288, C:L.315, C:L.315, E:I.253, E:P.254, E:L.256, E:L.257 Hydrogen bonds: C:S.291, C:R.295, E:I.249, E:Q.250 IVM.12: 12 residues within 4Å: Chain C: I.249, Q.250, I.253, P.254, L.256, L.257 Chain D: T.288, S.291, R.295, V.304, A.312, L.315 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:T.288, D:L.315, D:L.315, C:I.253, C:P.254, C:L.256, C:L.257 Hydrogen bonds: D:S.291, D:R.295, D:R.295, C:I.249, C:Q.250 IVM.15: 12 residues within 4Å: Chain B: I.249, Q.250, I.253, P.254, L.256, L.257 Chain E: T.288, S.291, R.295, V.304, A.312, L.315 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain E Hydrophobic interactions: B:I.253, B:P.254, B:L.256, B:L.257, E:T.288, E:V.304, E:L.315, E:L.315 Hydrogen bonds: B:I.249, B:Q.250, E:S.291, E:R.295, 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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