SMTL ID : 5vdi.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 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 B: 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 A, 3 interactions with chain B Hydrophobic interactions: A:I.28, A:F.32, A:Y.161, B:P.10 Hydrogen bonds: A:R.29, B:D.84 pi-Stacking: A:F.32, B: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 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:I.28, B:F.32, B:Y.161, C:P.10, C:L.83 Hydrogen bonds: B:R.29 pi-Stacking: B:F.32, C:Y.78 Water bridges: C:L.85, C:L.118 7C6.9: 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 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:P.10, D:L.83, C:I.28, C:F.32, C:Y.161 Water bridges: D:D.84, D:D.84 pi-Stacking: D:Y.78 Hydrogen bonds: C:R.29 7C6.13: 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 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:I.28, D:F.32, E:P.10 Hydrogen bonds: D:R.29 pi-Stacking: D:F.32, E:Y.78 7C6.17: 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 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 A Hydrophobic interactions: E:F.32, E:Y.161, A:P.10 Hydrogen bonds: E:R.29 pi-Stacking: E:F.32, A:Y.78

5 x GLY: GLYCINE(Non-covalent)

GLY.2: 8 residues within 4Å: Chain A: F.159, Y.202, T.204, F.207 Chain B: F.63, R.65, L.117, S.129 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:F.159, B:S.129, B:S.129 Salt bridges: B:R.65 GLY.6: 8 residues within 4Å: Chain B: F.159, Y.202, T.204, F.207 Chain C: F.63, R.65, L.117, S.129 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.129, B:F.159 Salt bridges: C:R.65 GLY.10: 7 residues within 4Å: Chain D: F.159, Y.202, T.204 Chain E: F.63, R.65, L.117, S.129 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:S.129, D:F.159, D:T.204, D:T.204 Salt bridges: E:R.65 GLY.14: 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:T.204 Salt bridges: D:R.65 GLY.18: 7 residues within 4Å: Chain A: F.63, R.65, L.117, S.129 Chain E: F.159, Y.202, T.204 6 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: E:F.159, E:T.204, A:S.129, G.18, G.18 Salt bridges: A:R.65

5 x IVM: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside(Non-covalent)

IVM.3: 15 residues within 4Å: Chain A: T.264, S.267, S.268, S.278, V.280, D.284, A.288, L.291, F.295 Chain B: I.225, Q.226, I.229, P.230, L.233, I.236 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.229, B:P.230, B:I.236, A:V.280, A:A.288, A:L.291, A:F.295 Hydrogen bonds: B:I.225, B:Q.226, A:S.267 IVM.7: 19 residues within 4Å: Chain B: T.264, S.267, S.268, S.278, Y.279, V.280, D.284, A.288, L.291, F.295 Chain C: G.221, L.224, I.225, Q.226, I.229, P.230, L.232, L.233, I.236 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:V.280, B:L.291, B:F.295, C:I.225, C:I.229, C:P.230, C:L.233, C:I.236 Hydrogen bonds: B:S.267, C:I.225, C:Q.226 IVM.11: 14 residues within 4Å: Chain C: T.264, S.267, S.278, V.280, D.284, A.288, L.291, F.295 Chain D: I.225, Q.226, I.229, P.230, L.232, L.233 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:V.280, C:L.291, C:F.295, D:I.225, D:I.229, D:P.230, D:L.232, D:L.233 Hydrogen bonds: C:S.267, D:I.225, D:Q.226 IVM.15: 12 residues within 4Å: Chain D: T.264, S.267, V.280, D.284, A.288, L.291, F.295 Chain E: I.225, Q.226, I.229, P.230, L.233 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:I.225, E:P.230, E:L.233, D:V.280, D:L.291, D:F.295 Hydrogen bonds: E:I.225, E:Q.226, D:S.267 IVM.19: 15 residues within 4Å: Chain A: I.225, Q.226, I.229, P.230, L.232, L.233, I.236 Chain E: T.264, S.267, S.268, V.280, D.284, A.288, L.291, F.295 10 PLIP interactions: 5 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:V.280, E:A.288, E:L.291, E:F.295, A:P.230, A:L.232, A:I.236 Hydrogen bonds: E:S.267, A:I.225, A:Q.226

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: E.192, D.194, H.215 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.194, A:D.194, A:H.215 ZN.8: 3 residues within 4Å: Chain B: E.192, D.194, H.215 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.192, B:D.194 ZN.12: 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.16: 3 residues within 4Å: Chain D: E.192, D.194, H.215 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.192, D:D.194 ZN.20: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, X. et al., Crystal Structures of Human GlyR alpha 3 Bound to Ivermectin. Structure (2017)

Release Date

2017-05-24

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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