SMTL ID : 5tio.1

Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-pentamer

Ligands

5 x 7C6: (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one(Non-covalent)

7C6.1: 16 residues within 4Å: Chain A: R.27, I.28, R.29, F.32, G.160, Y.161, D.165 Chain D: P.10, F.13, L.14, Y.78, D.80, L.83, D.84, L.85, D.86 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.28, A:F.32, A:Y.161, D:P.10 Hydrogen bonds: A:R.29 pi-Stacking: A:F.32, D:Y.78 7C6.5: 16 residues within 4Å: Chain B: R.27, I.28, R.29, F.32, G.160, Y.161, D.165 Chain C: P.10, F.13, L.14, Y.78, D.80, L.83, D.84, L.85, D.86 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.28, B:F.32, B:Y.161, C:P.10 Hydrogen bonds: B:R.29 pi-Stacking: B:F.32, C:Y.78 7C6.8: 16 residues within 4Å: Chain A: P.10, F.13, L.14, Y.78, D.80, L.83, D.84, L.85, D.86 Chain C: R.27, I.28, R.29, F.32, G.160, Y.161, D.165 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:P.10, C:I.28, C:F.32, C:Y.161 pi-Stacking: A:Y.78, C:F.32 Hydrogen bonds: C:R.29 7C6.11: 16 residues within 4Å: Chain D: R.27, I.28, R.29, F.32, G.160, Y.161, D.165 Chain E: P.10, F.13, L.14, Y.78, D.80, L.83, D.84, L.85, D.86 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:I.28, D:F.32, D:Y.161, E:P.10, E:L.83 Hydrogen bonds: D:R.29 pi-Stacking: D:F.32, E:Y.78 7C6.14: 15 residues within 4Å: Chain B: P.10, F.13, L.14, Y.78, L.83, D.84, L.85, D.86 Chain E: R.27, I.28, R.29, F.32, G.160, Y.161, D.165 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:I.28, E:F.32, B:P.10 Hydrogen bonds: E:R.29 pi-Stacking: E:F.32, B:Y.78

5 x GLY: GLYCINE(Non-covalent)

GLY.2: 7 residues within 4Å: Chain A: F.159, Y.202, T.204 Chain D: F.63, R.65, L.117, S.129 6 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: G.2, G.2, A:F.159, A:T.204, D:S.129 Salt bridges: D:R.65 GLY.6: 6 residues within 4Å: Chain B: F.159, Y.202, T.204 Chain C: F.63, 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.9: 7 residues within 4Å: Chain A: F.63, R.65, L.117, S.129 Chain C: F.159, Y.202, T.204 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:E.157, C:F.159, C:T.204, C:T.204, A:S.129 Salt bridges: A:R.65 GLY.13: 7 residues within 4Å: Chain D: F.159, Y.202, T.204 Chain E: F.63, R.65, L.117, S.129 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:S.129, D:F.159, D:T.204 Salt bridges: E:R.65 GLY.15: 6 residues within 4Å: Chain B: F.63, R.65, S.129 Chain E: F.159, T.204, F.207 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:F.159, B:S.129, B:S.129 Salt bridges: B:R.65

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: E.192, D.194, H.215 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.192, A:H.215 ZN.7: 3 residues within 4Å: Chain B: E.192, D.194, H.215 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.192, B:D.194, B:D.194, B:H.215 ZN.10: 3 residues within 4Å: Chain C: E.192, D.194, H.215 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.192, C:D.194, C:H.215 ZN.12: 3 residues within 4Å: Chain D: E.192, D.194, H.215 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.192, D:D.194, D:H.215 ZN.16: 3 residues within 4Å: Chain E: E.192, D.194, H.215 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.192, E:D.194, E:H.215

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

NAG.4: 3 residues within 4Å: Chain A: N.38, I.167, E.169 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.167 Hydrogen bonds: A:E.169, A:E.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, X. et al., Crystal Structures of Human GlyRa3 Bound to a Novel Class of Potentiators with Efficacy in a Mouse Model of Neuropathic Pain. To Be Published

Release Date

2017-01-18

Peptides

Glycine receptor subunit alpha-3: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Glycine receptor subunit alpha-3

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