SMTL ID : 8dn5.1

Cryo-EM structure of human Glycine Receptor alpha1-beta heteromer, glycine-bound state1(open state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

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

GLY.1: 7 residues within 4Å: Chain A: F.159, Y.202, T.204, F.207 Chain E: R.84, L.138, S.150 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: E:S.150, A:T.204, G.1, G.1 Salt bridges: E:R.84 GLY.13: 6 residues within 4Å: Chain B: F.159, Y.202, F.207 Chain C: F.63, R.65, S.129 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.129, C:S.129, C:S.129 Salt bridges: C:R.65 GLY.27: 7 residues within 4Å: Chain C: F.159, Y.202, T.204, F.207 Chain D: F.63, L.117, S.129 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.129 GLY.36: 8 residues within 4Å: Chain A: F.63, R.65, L.117, S.129 Chain D: F.159, Y.202, T.204, F.207 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:F.159, D:T.204, A:S.129 Salt bridges: A:R.65 GLY.45: 7 residues within 4Å: Chain B: F.63, R.65, S.129 Chain E: F.180, Y.223, T.226, Y.229 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:F.180, B:S.129 Salt bridges: B:R.65

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

NAG.2: 6 residues within 4Å: Chain A: N.31, P.35, P.36, N.38, I.167, E.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.31, A:N.38, A:E.169 NAG.14: 4 residues within 4Å: Chain B: N.31, P.35, P.36, N.38 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.31, B:N.38 NAG.28: 4 residues within 4Å: Chain C: P.35, P.36, N.38, E.169 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.38, C:N.38 NAG.37: 5 residues within 4Å: Chain D: P.35, P.36, N.38, I.167, E.169 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.167 Hydrogen bonds: D:E.169 NAG.46: 4 residues within 4Å: Chain E: T.184, N.218, T.220, Y.228 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.220

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

DD9.3: 6 residues within 4Å: Chain A: L.224, L.232, N.349, W.353, K.357 Ligands: HP6.4 No protein-ligand interaction detected (PLIP) DD9.17: 5 residues within 4Å: Chain B: I.285, F.348, Y.356 Ligands: HP6.18, NBU.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.285 DD9.21: 5 residues within 4Å: Chain B: I.240, W.243 Chain E: V.321, V.325, V.328 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:I.240, B:W.243, B:W.243, E:V.321 DD9.26: 4 residues within 4Å: Chain C: L.232 Ligands: D10.25, HEX.29, NBU.34 No protein-ligand interaction detected (PLIP)

6 x HP6: HEPTANE(Non-covalent)(Non-functional Binders)

HP6.4: 4 residues within 4Å: Chain A: M.350, W.353, K.357 Ligands: DD9.3 No protein-ligand interaction detected (PLIP) HP6.6: 7 residues within 4Å: Chain A: I.236, I.240, W.243 Chain D: L.299, A.303, F.306 Ligands: HEX.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.240, A:W.243, A:W.243, D:L.299 HP6.7: 6 residues within 4Å: Chain A: I.285, F.348, F.351, I.355, Y.356 Ligands: HEX.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.351, A:F.351 HP6.18: 2 residues within 4Å: Ligands: DD9.17, D10.25 No protein-ligand interaction detected (PLIP) HP6.38: 3 residues within 4Å: Chain D: M.350, K.357 Ligands: HP6.39 No protein-ligand interaction detected (PLIP) HP6.39: 6 residues within 4Å: Chain D: M.220, L.224, N.349, W.353 Ligands: HP6.38, NBU.40 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.224, D:W.353, D:W.353

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

HEX.5: 2 residues within 4Å: Chain A: W.243 Ligands: HP6.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.243 HEX.8: 4 residues within 4Å: Chain A: V.280 Ligands: HP6.7, NBU.44, UND.48 No protein-ligand interaction detected (PLIP) HEX.9: 4 residues within 4Å: Chain A: I.336, F.341, A.344 Ligands: HEX.10 No protein-ligand interaction detected (PLIP) HEX.10: 4 residues within 4Å: Chain A: L.299, E.300, A.303 Ligands: HEX.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.299, A:E.300 HEX.11: 3 residues within 4Å: Chain A: A.303, F.306 Chain E: W.265 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:F.306, E:W.265 HEX.19: 6 residues within 4Å: Chain B: F.293, S.296, S.337, F.341, A.344 Ligands: NBU.20 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.341 HEX.29: 6 residues within 4Å: Chain C: L.224, N.349, W.353 Ligands: DD9.26, HEX.30, NBU.34 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.224 HEX.30: 5 residues within 4Å: Chain C: N.349, M.350, W.353, I.354 Ligands: HEX.29 No protein-ligand interaction detected (PLIP) HEX.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.41: 2 residues within 4Å: Chain D: I.225 Ligands: NBU.40 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.225, D:I.225 HEX.42: 5 residues within 4Å: Chain D: I.285, F.348, I.355, Y.356 Ligands: NBU.43 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.356 HEX.51: 2 residues within 4Å: Chain E: W.261, W.265 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.265 HEX.52: 4 residues within 4Å: Chain E: I.656, Y.659, L.663, F.664 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.664

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

UND.12: 4 residues within 4Å: Chain A: I.225, I.229 Chain D: A.288 Ligands: NBU.43 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.225 UND.15: 8 residues within 4Å: Chain B: M.220, L.224, L.232, N.349, W.353, K.357 Ligands: UND.16, UND.24 No protein-ligand interaction detected (PLIP) UND.16: 5 residues within 4Å: Chain B: L.346, M.350, W.353, K.357 Ligands: UND.15 No protein-ligand interaction detected (PLIP) UND.23: 9 residues within 4Å: Chain B: G.221, I.225, I.229 Chain E: S.300, Y.301, V.302, I.310 Ligands: UND.24, D10.47 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.302 UND.24: 4 residues within 4Å: Chain B: I.229, L.232 Ligands: UND.15, UND.23 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.229 UND.48: 6 residues within 4Å: Chain A: S.278, A.288 Chain E: M.246, M.247, A.251 Ligands: HEX.8 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.251

8 x NBU: N-BUTANE(Non-covalent)(Non-functional Binders)

NBU.20: 4 residues within 4Å: Chain B: S.296, L.299, E.300 Ligands: HEX.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.299 NBU.22: 2 residues within 4Å: Chain B: I.355 Ligands: DD9.17 No protein-ligand interaction detected (PLIP) NBU.31: 2 residues within 4Å: Chain C: W.239, I.240 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.239 NBU.33: 2 residues within 4Å: Chain C: V.289 Ligands: D10.32 No protein-ligand interaction detected (PLIP) NBU.34: 2 residues within 4Å: Ligands: DD9.26, HEX.29 No protein-ligand interaction detected (PLIP) NBU.40: 2 residues within 4Å: Ligands: HP6.39, HEX.41 No protein-ligand interaction detected (PLIP) NBU.43: 4 residues within 4Å: Chain D: V.280, I.285 Ligands: UND.12, HEX.42 No protein-ligand interaction detected (PLIP) NBU.44: 1 residues within 4Å: Ligands: HEX.8 No protein-ligand interaction detected (PLIP)

3 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.25: 5 residues within 4Å: Chain B: Y.279 Chain C: G.221, I.225 Ligands: HP6.18, DD9.26 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.225 D10.32: 5 residues within 4Å: Chain C: V.280, I.285, F.348, F.351 Ligands: NBU.33 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.280 D10.47: 7 residues within 4Å: Chain E: V.302, V.307, I.310, A.311, L.314, Y.679 Ligands: UND.23 No protein-ligand interaction detected (PLIP)

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

OCT.49: 4 residues within 4Å: Chain E: M.246, Y.250, W.676 Ligands: OCT.50 No protein-ligand interaction detected (PLIP) OCT.50: 4 residues within 4Å: Chain E: N.672, V.673, W.676 Ligands: OCT.49 No protein-ligand interaction detected (PLIP)

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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