SMTL ID : 5obg.1

Crystal structure of glycine binding protein in complex with strychnine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-pentamer

Ligands

5 x SY9: STRYCHNINE(Non-covalent)

SY9.1: 15 residues within 4Å: Chain A: E.162, S.163, W.164, V.165, Y.166, S.167, Y.205, T.208, E.210, Y.212 Chain B: Y.72, R.74, R.96, V.125, S.135 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.164, A:Y.205, A:Y.205, A:Y.212, A:Y.212 Salt bridges: A:E.162 pi-Cation interactions: A:Y.212 Hydrogen bonds: B:R.74, B:S.135 SY9.12: 14 residues within 4Å: Chain B: E.162, S.163, W.164, V.165, Y.166, Y.205, T.208, E.210, Y.212 Chain C: Y.72, R.74, S.135 Ligands: ACT.22, EDO.23 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.164, B:Y.205, B:Y.205, B:Y.205, B:Y.205, B:Y.205, B:E.210, B:Y.212, B:Y.212 Salt bridges: B:E.162 Hydrogen bonds: C:R.74, C:S.135 SY9.24: 13 residues within 4Å: Chain C: E.162, S.163, W.164, V.165, S.167, Y.205, T.208, E.210, Y.212 Chain D: Y.72, R.96, V.125, S.135 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:Y.72, C:W.164, C:Y.205, C:Y.205, C:Y.212, C:Y.212 Hydrogen bonds: D:S.135 Salt bridges: C:E.162 pi-Cation interactions: C:Y.212 SY9.33: 12 residues within 4Å: Chain D: E.162, S.163, W.164, V.165, Y.166, S.167, Y.205, E.210, Y.212 Chain E: Y.72 Ligands: ACT.35, EDO.44 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:W.164, D:Y.205, D:Y.205, D:Y.205, D:Y.205, D:Y.205, D:E.210, D:Y.212, D:Y.212 Salt bridges: D:E.162 Water bridges: E:S.135 SY9.45: 15 residues within 4Å: Chain A: Y.72, R.74, S.135 Chain E: E.162, S.163, W.164, V.165, Y.166, S.167, Y.205, T.208, E.210, Y.212 Ligands: ACT.10, EDO.11 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:W.164, E:Y.205, E:Y.205, E:Y.205, E:Y.205, E:E.210, E:Y.212, E:Y.212 Salt bridges: E:E.162 Hydrogen bonds: A:S.135

31 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: V.118, L.119 Chain E: T.108, A.109, S.112, R.114, P.115, V.116 Ligands: NA.42 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: M.36, Y.37, L.79, S.81, L.82, I.102, W.103 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: V.118, Q.122, F.134, P.136, Q.138 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: Q.179, V.180, L.182, S.195, A.196, T.197 Ligand excluded by PLIP EDO.8: 10 residues within 4Å: Chain A: T.108, A.109, S.112, R.114, P.115, V.116 Chain B: V.118, L.119 Ligands: NA.6, ACT.7 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: P.38, P.40, T.41, Y.166, E.170 Chain B: L.23, D.94, F.95, R.96 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: R.74, V.125, M.133, S.135 Ligands: ACT.10, SY9.45 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: W.103, Y.166 Chain C: T.97, S.98, I.123 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain B: M.36, Y.37, L.79, S.81, L.82, I.102, W.103 Ligands: EDO.17 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: Q.179, S.195, A.196 Ligand excluded by PLIP EDO.17: 9 residues within 4Å: Chain B: S.34, P.35, M.36, Y.37, P.38, S.81 Chain C: Q.20, M.24 Ligands: EDO.15 Ligand excluded by PLIP EDO.20: 10 residues within 4Å: Chain B: T.108, A.109, S.112, R.114, P.115, V.116 Chain C: V.118, L.119 Ligands: NA.18, ACT.19 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain B: P.38, P.40, T.41, Y.166, E.170 Chain C: L.23, D.94, F.95, R.96 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: V.165 Chain C: R.96, V.125, M.133 Ligands: SY9.12, ACT.22 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: W.103, Y.166 Chain D: S.98 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain C: Y.37, L.79, S.81, L.82, I.102, W.103 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain C: N.65, D.145, T.147 Chain D: S.188, S.189, K.190, R.224 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: S.111, M.143 Chain C: Q.55, S.184, Y.186 Ligand excluded by PLIP EDO.32: 9 residues within 4Å: Chain C: T.108, A.109, S.112, R.114, P.115, V.116 Chain D: V.118, L.119 Ligands: NA.30 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain D: Y.37, L.79, S.81, L.82, I.102, W.103 Ligands: EDO.40 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain D: Y.37, L.79, N.80, S.81 Chain E: Q.20 Ligand excluded by PLIP EDO.38: 8 residues within 4Å: Chain C: P.38, P.40, Y.166, E.170 Chain D: L.23, D.94, F.95, R.96 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain D: N.65, D.145, T.147 Chain E: S.188, S.189, R.224 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain D: L.30, F.31, S.34, P.35, M.36 Ligands: EDO.36 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain E: R.74, V.125, M.133 Ligands: SY9.33, ACT.35 Ligand excluded by PLIP EDO.49: 9 residues within 4Å: Chain D: T.108, A.109, S.112, R.114, P.115, V.116 Chain E: V.118, L.119 Ligands: NA.41 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain A: R.96, T.97, S.98 Chain E: P.38, W.103, Y.166 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain A: Q.20 Chain E: Y.37, L.79, N.80, S.81 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain A: S.188, S.189, K.190, R.224 Chain E: N.65, D.145, T.147 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain D: S.111, M.143 Chain E: Q.55, S.184, Y.186 Ligand excluded by PLIP EDO.54: 7 residues within 4Å: Chain E: M.36, Y.37, L.79, S.81, L.82, I.102, W.103 Ligand excluded by PLIP

5 x NA: SODIUM ION(Non-functional Binders)

NA.6: 6 residues within 4Å: Chain A: T.108, A.109, S.112 Chain B: L.119 Ligands: ACT.7, EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.112, A:S.112 NA.18: 6 residues within 4Å: Chain B: T.108, A.109, S.112 Chain C: L.119 Ligands: ACT.19, EDO.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.109 NA.30: 6 residues within 4Å: Chain C: T.108, A.109, S.112 Chain D: L.119 Ligands: ACT.31, EDO.32 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.119 NA.41: 6 residues within 4Å: Chain D: T.108, A.109, S.112 Chain E: L.119 Ligands: ACT.47, EDO.49 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.109 NA.42: 6 residues within 4Å: Chain A: L.119 Chain E: T.108, A.109, S.112 Ligands: EDO.2, ACT.43 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:L.119 Water bridges: E:T.108

9 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 11 residues within 4Å: Chain A: A.109, A.110, S.111, S.112, M.143 Chain B: Q.55, V.70, L.119, A.137 Ligands: NA.6, EDO.8 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.112, A:S.112, B:Q.55 Water bridges: A:T.108 Hydrophobic interactions: B:V.70 ACT.10: 5 residues within 4Å: Chain A: S.135 Chain E: W.164, V.165 Ligands: EDO.11, SY9.45 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:W.164 Water bridges: A:S.135, A:S.135 ACT.19: 10 residues within 4Å: Chain B: A.109, A.110, S.111, S.112 Chain C: Q.55, V.70, L.119, A.137 Ligands: NA.18, EDO.20 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:V.70, C:L.119 Hydrogen bonds: C:Q.55, B:S.112, B:S.112 Water bridges: B:T.108 ACT.22: 5 residues within 4Å: Chain B: W.164, V.165 Chain C: S.135 Ligands: SY9.12, EDO.23 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.165 Hydrogen bonds: B:W.164 Water bridges: C:S.135 ACT.31: 9 residues within 4Å: Chain C: A.109, A.110, S.111, S.112 Chain D: Q.55, V.70, L.119, A.137 Ligands: NA.30 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.112, D:Q.55, D:Q.55 Hydrophobic interactions: D:V.70 ACT.35: 6 residues within 4Å: Chain D: W.164, V.165 Chain E: M.133, S.135 Ligands: SY9.33, EDO.44 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.135, D:W.164 ACT.43: 10 residues within 4Å: Chain A: Q.55, V.70, L.119, A.137 Chain E: A.109, A.110, S.111, S.112, M.143 Ligands: NA.42 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:V.70, A:L.119 Hydrogen bonds: A:Q.55, E:S.112, E:S.112 Water bridges: E:T.108 ACT.47: 9 residues within 4Å: Chain D: A.109, A.110, S.111, S.112 Chain E: Q.55, V.70, L.119, A.137 Ligands: NA.41 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:S.112, E:Q.55, E:Q.55 Water bridges: D:T.108 Hydrophobic interactions: E:V.70 ACT.48: 3 residues within 4Å: Chain E: P.45, T.47, G.168 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:P.45 Hydrogen bonds: E:T.47

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

NAG.13: 2 residues within 4Å: Chain B: N.87, N.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.87 NAG.25: 3 residues within 4Å: Chain B: D.43 Chain C: G.90, N.91 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.91 NAG.34: 1 residues within 4Å: Chain D: N.91 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.91 NAG.46: 1 residues within 4Å: Chain E: N.91 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dawson, A. et al., Engineering a surrogate human heteromeric alpha / beta glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein. Iucrj (2019)

Release Date

2018-08-01

Peptides

Soluble acetylcholine receptor: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Soluble acetylcholine receptor

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