SMTL ID : 5tin.1

Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 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: 15 residues within 4Å: Chain A: R.27, I.28, R.29, F.32, G.160, Y.161, D.165 Chain B: P.10, F.13, L.14, Y.78, L.83, D.84, L.85, D.86 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.32, A:Y.161, B:P.10 Hydrogen bonds: A:R.29 pi-Stacking: A:F.32, B:Y.78 Water bridges: B:D.84, B:L.85 7C6.4: 15 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, L.83, D.84, L.85, D.86 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.32, C:P.10, C:L.83 Hydrogen bonds: B:R.29 Water bridges: B:D.165, C:D.84, C:L.85 pi-Stacking: C:Y.78 7C6.7: 15 residues within 4Å: Chain C: R.27, I.28, R.29, F.32, G.160, Y.161, D.165 Chain D: P.10, F.13, L.14, Y.78, L.83, D.84, L.85, D.86 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.28, C:F.32, C:Y.161, D:P.10 Hydrogen bonds: C:R.29 Water bridges: C:D.165 pi-Stacking: D:Y.78 7C6.10: 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 10 PLIP interactions: 5 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:P.10, E:L.83, D:F.32, D:Y.161 Water bridges: E:D.84, E:D.86, D:D.97, D:D.165 pi-Stacking: E:Y.78 Hydrogen bonds: D:R.29 7C6.13: 15 residues within 4Å: Chain A: 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 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:P.10, E:F.32, E:Y.161 Water bridges: A:D.84, A:L.85 pi-Stacking: A:Y.78 Hydrogen bonds: E:R.29

5 x GLY: GLYCINE(Non-covalent)

GLY.2: 7 residues within 4Å: Chain A: F.159, Y.202, T.204, F.207 Chain B: F.63, R.65, S.129 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.129, A:T.204 Salt bridges: B:R.65 GLY.5: 7 residues within 4Å: Chain B: F.159, Y.202, T.204, F.207 Chain C: F.63, R.65, S.129 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:F.159, C:S.129, C:S.129 Salt bridges: C:R.65 GLY.9: 8 residues within 4Å: Chain C: F.159, Y.202, T.204, F.207 Chain D: F.63, R.65, L.117, S.129 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.129, C:F.159 Salt bridges: D:R.65 GLY.11: 8 residues within 4Å: Chain D: F.159, Y.202, T.204, F.207 Chain E: F.63, R.65, L.117, S.129 6 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: E:S.129, D:T.204, D:T.204, D:T.204, G.11 Salt bridges: E:R.65 GLY.14: 7 residues within 4Å: Chain A: F.63, R.65, S.129 Chain E: F.159, Y.202, T.204, F.207 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:F.159, E:T.204, E:T.204, A:S.129 Salt bridges: A:R.65

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: E.192, D.194, H.215 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.192, A:D.194, A:D.194, A:H.215 ZN.6: 3 residues within 4Å: Chain B: E.192, D.194, H.215 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.192, B:D.194, B:H.215 ZN.8: 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 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.192, E:D.194, E:H.215, H2O.15

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

CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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
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 alpha-3

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