SMTL ID : 8dn2.1

Cryo-EM structure of human Glycine Receptor alpha1-beta heteromer, glycine-bound state 2(expanded open)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: P.35, P.36, N.38, I.167 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.167 NAG.12: 4 residues within 4Å: Chain B: P.35, P.36, N.38, I.167 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.36, B:P.36, B:N.38, B:N.38 NAG.23: 4 residues within 4Å: Chain C: P.35, P.36, N.38, I.167 No protein-ligand interaction detected (PLIP) NAG.28: 2 residues within 4Å: Chain D: P.36, N.38 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.36, D:N.38 NAG.36: 4 residues within 4Å: Chain E: T.184, R.188, N.218, T.220 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.184, E:N.218, E:T.220

10 x HEX: HEXANE(Non-functional Binders)(Non-covalent)(Covalent)

HEX.2: 1 residues within 4Å: Ligands: HP6.6 No protein-ligand interaction detected (PLIP) HEX.4: 4 residues within 4Å: Chain A: I.285, I.355, Y.356 Ligands: HP6.3 No protein-ligand interaction detected (PLIP) HEX.5: 1 residues within 4Å: Chain A: I.354 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.354 HEX.13: 5 residues within 4Å: Chain B: M.350, W.353, I.354, K.357 Ligands: UND.14 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.353 HEX.19: 4 residues within 4Å: Chain B: I.285, V.289, F.348 Ligands: NBU.16 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.285, B:F.348 HEX.20: 4 residues within 4Å: Chain B: R.329, I.333, I.336 Ligands: OCT.18 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.333, B:I.336 HEX.21: 3 residues within 4Å: Chain C: M.350, W.353 Ligands: UND.24 No protein-ligand interaction detected (PLIP) HEX.26: 4 residues within 4Å: Chain C: I.285, F.348, I.355, Y.356 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.285 HEX.35: 3 residues within 4Å: Chain D: F.351, I.354 Ligands: NBU.32 No protein-ligand interaction detected (PLIP) HEX.38: 4 residues within 4Å: Chain E: F.671, Y.679 Ligands: D10.37, DD9.39 No protein-ligand interaction detected (PLIP)

9 x HP6: HEPTANE(Non-covalent)(Non-functional Binders)(Covalent)

HP6.3: 3 residues within 4Å: Chain A: I.285, V.289 Ligands: HEX.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.285 HP6.6: 4 residues within 4Å: Chain A: M.350, K.357 Ligands: HEX.2, UND.7 No protein-ligand interaction detected (PLIP) HP6.8: 2 residues within 4Å: Chain A: L.224, I.225 No protein-ligand interaction detected (PLIP) HP6.9: 1 residues within 4Å: Chain A: I.339 No protein-ligand interaction detected (PLIP) HP6.25: 2 residues within 4Å: Chain C: I.229 Ligands: UND.24 No protein-ligand interaction detected (PLIP) HP6.29: 6 residues within 4Å: Chain D: K.143, I.285, F.348, F.351, I.355, Y.356 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.285, D:I.355 HP6.31: 6 residues within 4Å: Chain D: M.350, W.353, I.354, K.357 Ligands: OCT.30, OCT.33 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.353 HP6.41: 3 residues within 4Å: Chain E: N.672, V.673, W.676 No protein-ligand interaction detected (PLIP) HP6.43: 2 residues within 4Å: Chain E: W.265, P.665 No protein-ligand interaction detected (PLIP)

3 x UND: UNDECANE(Non-covalent)(Covalent)

UND.7: 6 residues within 4Å: Chain A: M.220, L.224, N.349, W.353, K.357 Ligands: HP6.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.353 UND.14: 6 residues within 4Å: Chain B: M.220, L.224, L.232, N.349, W.353 Ligands: HEX.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.232, B:W.353, B:W.353 UND.24: 6 residues within 4Å: Chain C: M.220, N.349, W.353, K.357 Ligands: HEX.21, HP6.25 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.353, C:W.353

7 x OCT: N-OCTANE(Covalent)(Non-covalent)(Non-functional Binders)

OCT.10: 3 residues within 4Å: Chain A: L.299, E.300, I.333 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.300 OCT.17: 3 residues within 4Å: Chain B: I.336, I.339, G.340 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.336, B:I.336 OCT.18: 6 residues within 4Å: Chain B: S.296, L.299, E.300, A.303, I.333 Ligands: HEX.20 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.299, B:A.303 OCT.30: 4 residues within 4Å: Chain D: I.354, I.358 Ligands: HP6.31, NBU.32 No protein-ligand interaction detected (PLIP) OCT.33: 1 residues within 4Å: Ligands: HP6.31 No protein-ligand interaction detected (PLIP) OCT.40: 1 residues within 4Å: Ligands: DD9.39 No protein-ligand interaction detected (PLIP) OCT.42: 3 residues within 4Å: Chain A: A.303, F.306 Chain E: W.265 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.265, E:W.265

3 x GLY: GLYCINE(Non-covalent)(Covalent)

GLY.11: 5 residues within 4Å: Chain B: F.159, T.204, F.207 Chain C: R.65, S.129 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.129, C:S.129, B:F.159 Salt bridges: C:R.65 GLY.22: 7 residues within 4Å: Chain C: F.159, T.204, F.207 Chain D: F.63, R.65, L.117, S.129 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.65 GLY.27: 4 residues within 4Å: Chain A: F.63, R.65, S.129 Chain D: F.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.129 Salt bridges: A:R.65

2 x DD9: nonane(Non-functional Binders)(Non-covalent)

DD9.15: 4 residues within 4Å: Chain B: I.225, I.229 Chain E: V.302 Ligands: D10.37 No protein-ligand interaction detected (PLIP) DD9.39: 4 residues within 4Å: Chain E: I.674, I.678 Ligands: HEX.38, OCT.40 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.678

3 x NBU: N-BUTANE(Non-functional Binders)

NBU.16: 3 residues within 4Å: Chain B: I.285, V.289 Ligands: HEX.19 No protein-ligand interaction detected (PLIP) NBU.32: 2 residues within 4Å: Ligands: OCT.30, HEX.35 No protein-ligand interaction detected (PLIP) NBU.34: 2 residues within 4Å: Chain C: V.280 Chain D: I.225 No protein-ligand interaction detected (PLIP)

1 x D10: DECANE(Non-covalent)

D10.37: 5 residues within 4Å: Chain E: V.302, V.307, Y.679 Ligands: DD9.15, HEX.38 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Asymmetric gating of a human hetero-pentameric glycine receptor. Nat Commun (2023)

Release Date

2023-10-11

Peptides

Glycine receptor subunit alpha-1: ABCD
Glycine receptor subunit beta,Green fluorescent protein,Glycine receptor beta: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

E
E

Membrane

We predict this structure to be a membrane protein.
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Glycine receptor subunit alpha-1

Glycine receptor subunit beta,Green fluorescent protein,Glycine receptor beta

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