SMTL ID : 8dn3.1

Cryo-EM structure of human Glycine Receptor alpha1-beta heteromer, apo state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: N.31, P.35, P.36, V.37, N.38, I.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.31, A:N.38 NAG.14: 5 residues within 4Å: Chain B: N.31, P.35, P.36, N.38, I.167 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.31, B:N.38 NAG.26: 3 residues within 4Å: Chain C: P.35, P.36, N.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.36 NAG.38: 7 residues within 4Å: Chain D: N.31, P.35, P.36, V.37, N.38, I.167, E.169 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.38, D:N.38 NAG.52: 3 residues within 4Å: Chain E: R.188, I.190, N.218 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.190 Hydrogen bonds: E:R.188

15 x HEX: HEXANE(Non-functional Binders)(Non-covalent)

HEX.2: 2 residues within 4Å: Ligands: UND.3, HEX.13 No protein-ligand interaction detected (PLIP) HEX.7: 2 residues within 4Å: Chain A: I.355 Ligands: HP6.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.355 HEX.13: 5 residues within 4Å: Chain A: G.221, L.224, I.225 Ligands: HEX.2, HEX.39 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.224 HEX.19: 5 residues within 4Å: Chain B: I.285, F.348, I.355, Y.356 Ligands: HEX.20 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.348 HEX.20: 4 residues within 4Å: Chain B: I.285, V.289 Chain C: I.225 Ligands: HEX.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.285, B:V.289 HEX.23: 3 residues within 4Å: Chain B: F.306 Chain C: W.243 Ligands: UND.22 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.243, B:F.306 HEX.25: 2 residues within 4Å: Ligands: HP6.17, DD9.24 No protein-ligand interaction detected (PLIP) HEX.27: 3 residues within 4Å: Ligands: DD9.32, DD9.35, HP6.46 No protein-ligand interaction detected (PLIP) HEX.28: 2 residues within 4Å: Chain C: L.224 Ligands: DD9.29 No protein-ligand interaction detected (PLIP) HEX.31: 2 residues within 4Å: Chain C: W.243, I.339 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.243 HEX.39: 5 residues within 4Å: Chain A: I.225 Chain D: I.285, A.288 Ligands: HEX.13, D10.42 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.285 HEX.41: 1 residues within 4Å: Ligands: UND.40 No protein-ligand interaction detected (PLIP) HEX.43: 4 residues within 4Å: Chain D: I.339, G.340, M.343, A.344 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.339 HEX.50: 4 residues within 4Å: Chain E: G.243, M.246, M.247 Ligands: HP6.49 No protein-ligand interaction detected (PLIP) HEX.57: 3 residues within 4Å: Chain E: V.325, M.329 Ligands: DD9.56 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.325

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

UND.3: 6 residues within 4Å: Chain A: M.220, L.224, L.232, N.349, W.353 Ligands: HEX.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.224, A:L.232 UND.4: 6 residues within 4Å: Chain A: N.349, M.350, W.353, I.354, K.357, I.358 No protein-ligand interaction detected (PLIP) UND.11: 8 residues within 4Å: Chain A: S.296, L.299, E.300, A.303, R.329, I.333 Ligands: NBU.10, UND.12 No protein-ligand interaction detected (PLIP) UND.12: 7 residues within 4Å: Chain A: L.299, F.306, V.307 Chain E: L.262, W.265 Ligands: UND.11, HP6.51 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.299, A:F.306 UND.15: 9 residues within 4Å: Chain B: I.236, W.239, I.240, W.243 Chain E: V.321, A.324, V.328, M.329 Ligands: UND.16 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:I.240, E:V.328 UND.16: 4 residues within 4Å: Chain B: W.239, W.243, I.339 Ligands: UND.15 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.339 UND.22: 8 residues within 4Å: Chain B: S.296, L.299, E.300, A.303, R.329, F.341 Ligands: DD9.21, HEX.23 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.299, B:E.300 UND.40: 7 residues within 4Å: Chain A: I.236, I.240, W.243 Chain D: L.299, F.306 Ligands: DD9.5, HEX.41 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.240, A:W.243, D:L.299, D:F.306 UND.44: 7 residues within 4Å: Chain D: F.293, S.296, I.333, I.336, S.337, F.341 Ligands: UND.45 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.336, D:F.341, D:F.341, D:F.341 UND.45: 7 residues within 4Å: Chain D: S.296, L.299, E.300, A.303, R.329, I.333 Ligands: UND.44 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.303 UND.54: 6 residues within 4Å: Chain E: L.669, N.672, V.673, W.676, L.680 Ligands: NBU.53 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.669, E:L.680 UND.59: 5 residues within 4Å: Chain E: V.302, V.307, I.310 Ligands: DD9.24, NBU.58 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.307

13 x DD9: nonane(Non-covalent)(Covalent)(Non-functional Binders)

DD9.5: 4 residues within 4Å: Chain A: W.243, R.338, I.339 Ligands: UND.40 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.243, A:I.339 DD9.21: 8 residues within 4Å: Chain B: F.293, S.296, I.336, S.337, G.340, F.341, A.344 Ligands: UND.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.341 DD9.24: 7 residues within 4Å: Chain B: L.224, I.225, I.229 Chain E: V.302, L.314 Ligands: HEX.25, UND.59 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.224 DD9.29: 7 residues within 4Å: Chain C: L.224, L.232, N.349, W.353, K.357 Ligands: HEX.28, DD9.30 No protein-ligand interaction detected (PLIP) DD9.30: 6 residues within 4Å: Chain C: N.349, M.350, W.353, K.357, I.358 Ligands: DD9.29 No protein-ligand interaction detected (PLIP) DD9.32: 7 residues within 4Å: Chain C: S.296, L.299, E.300, A.303, I.333 Ligands: HEX.27, DD9.35 No protein-ligand interaction detected (PLIP) DD9.34: 5 residues within 4Å: Chain C: I.285, F.348, I.355, Y.356 Ligands: DD9.36 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.348 DD9.35: 6 residues within 4Å: Chain C: L.299, F.306 Chain D: W.243 Ligands: HEX.27, DD9.32, HP6.46 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.299, C:F.306 DD9.36: 7 residues within 4Å: Chain C: I.285, V.289 Chain D: G.221, L.224, I.225 Ligands: DD9.34, HP6.37 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.289, D:I.225 DD9.47: 6 residues within 4Å: Chain D: L.346, N.349, M.350, W.353, K.357 Ligands: DD9.48 No protein-ligand interaction detected (PLIP) DD9.48: 5 residues within 4Å: Chain D: L.232, N.349, W.353, K.357 Ligands: DD9.47 No protein-ligand interaction detected (PLIP) DD9.55: 4 residues within 4Å: Chain E: A.662, L.663, F.666, C.667 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.663, E:F.666, E:F.666 DD9.56: 7 residues within 4Å: Chain E: A.318, V.321, E.322, Y.659, L.663, F.664 Ligands: HEX.57 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.659, E:L.663

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

NBU.6: 2 residues within 4Å: Chain A: F.351, I.354 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.351, A:I.354 NBU.10: 6 residues within 4Å: Chain A: I.336, S.337, G.340, F.341 Ligands: HP6.9, UND.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.341 NBU.33: 3 residues within 4Å: Chain C: I.339, G.340, M.343 No protein-ligand interaction detected (PLIP) NBU.53: 2 residues within 4Å: Chain E: M.246 Ligands: UND.54 No protein-ligand interaction detected (PLIP) NBU.58: 4 residues within 4Å: Chain E: V.307, I.678, Y.679 Ligands: UND.59 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.679

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

HP6.8: 5 residues within 4Å: Chain A: F.348, I.355, Y.356 Ligands: HEX.7, HP6.49 No protein-ligand interaction detected (PLIP) HP6.9: 4 residues within 4Å: Chain A: I.336, I.339, M.343 Ligands: NBU.10 No protein-ligand interaction detected (PLIP) HP6.17: 6 residues within 4Å: Chain B: L.224, L.232, W.353, K.357 Ligands: HP6.18, HEX.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.224, B:L.232 HP6.18: 4 residues within 4Å: Chain B: M.350, W.353, I.358 Ligands: HP6.17 No protein-ligand interaction detected (PLIP) HP6.37: 3 residues within 4Å: Chain D: I.225, I.229 Ligands: DD9.36 No protein-ligand interaction detected (PLIP) HP6.46: 5 residues within 4Å: Chain D: W.239, W.243, I.339 Ligands: HEX.27, DD9.35 No protein-ligand interaction detected (PLIP) HP6.49: 6 residues within 4Å: Chain A: V.280, I.285, V.289 Chain E: M.247 Ligands: HP6.8, HEX.50 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.285, A:V.289 HP6.51: 3 residues within 4Å: Chain E: R.661, P.665 Ligands: UND.12 No protein-ligand interaction detected (PLIP)

1 x D10: DECANE(Non-covalent)

D10.42: 4 residues within 4Å: Chain D: F.348, I.355, Y.356 Ligands: HEX.39 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.355, D:Y.356

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.61: 1 residues within 4Å: Chain E: T.291 Ligand excluded by 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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