SMTL ID : 3jaf.1

Structure of alpha-1 glycine receptor by single particle electron cryo-microscopy, glycine/ivermectin-bound state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.80 Å

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: 3 residues within 4Å: Chain A: P.27, P.28, N.30 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: P.27, P.28, N.30 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: P.27, P.28, N.30 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain D: P.27, P.28, N.30 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain E: P.27, P.28, N.30 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.6: 13 residues within 4Å: Chain A: T.256, S.259, R.263, V.272, A.280, L.283 Chain B: L.216, I.217, I.221, P.222, L.224, L.225, I.228 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.256, A:V.272, A:L.283, B:P.222, B:L.224, B:I.228 Hydrogen bonds: A:S.259, A:R.263, A:R.263, B:I.217 IVM.7: 14 residues within 4Å: Chain B: T.256, S.259, R.263, Y.271, V.272, A.280, L.283 Chain C: L.216, I.217, I.221, P.222, L.224, L.225, I.228 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:T.256, B:V.272, B:L.283, C:P.222, C:L.224, C:I.228 Hydrogen bonds: B:S.259, B:R.263, B:R.263, B:S.270, C:I.217 IVM.8: 14 residues within 4Å: Chain C: T.256, S.259, R.263, V.272, A.280, L.283, L.284 Chain D: L.216, I.217, I.221, P.222, L.224, L.225, I.228 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:T.256, C:V.272, C:L.283, C:L.284, D:P.222, D:L.224, D:I.228 Hydrogen bonds: C:S.259, C:R.263, C:R.263, D:I.217 IVM.9: 13 residues within 4Å: Chain D: T.256, S.259, R.263, V.272, A.280, L.283 Chain E: L.216, I.217, I.221, P.222, L.224, L.225, I.228 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:P.222, E:L.224, E:I.228, D:T.256, D:V.272, D:L.283 Hydrogen bonds: E:I.217, D:S.259, D:R.263, D:R.263 IVM.10: 13 residues within 4Å: Chain A: L.216, I.217, I.221, P.222, L.224, L.225, I.228 Chain E: T.256, S.259, R.263, V.272, A.280, L.283 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:P.222, A:L.224, A:I.228, E:T.256, E:V.272, E:L.283 Hydrogen bonds: A:I.217, E:S.259, E:R.263, E:R.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, J. et al., Glycine receptor mechanism elucidated by electron cryo-microscopy. Nature (2015)

Release Date

2015-09-09

Peptides

Glycine receptor subunit alphaZ1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

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

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