SMTL ID : 5oa0.1

Crystal structure of mutant AChBP in complex with strychnine (T53F, Q74R, Y110A, I135S, W164F)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-pentamer

Ligands

5 x SY9: STRYCHNINE(Non-covalent)

SY9.1: 11 residues within 4Å: Chain A: S.163, F.164, Y.205, C.207, C.208, Y.212 Chain B: F.53, Y.72, R.74, S.135, S.184 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.72, B:Y.72, A:F.164, A:Y.205, A:Y.212 Hydrogen bonds: B:S.184 pi-Stacking: B:F.53 SY9.9: 11 residues within 4Å: Chain B: S.163, F.164, Y.205, C.207, C.208 Chain C: F.53, Y.72, R.74, M.133, S.135, S.184 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.72, C:Y.72, B:F.164, B:Y.205 pi-Stacking: C:F.53 SY9.10: 11 residues within 4Å: Chain C: S.163, F.164, Y.205, C.207, C.208, Y.212 Chain D: F.53, Y.72, R.74, S.135, S.184 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.164, C:Y.205, C:Y.212, D:Y.72, D:Y.72 Hydrogen bonds: D:S.184 pi-Stacking: D:F.53 SY9.13: 12 residues within 4Å: Chain D: S.163, F.164, Y.205, C.207, C.208, Y.212 Chain E: F.53, Y.72, R.74, M.133, S.135, S.184 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:Y.72, E:Y.72, D:F.164, D:Y.205 Hydrogen bonds: E:S.184 pi-Stacking: E:F.53 SY9.16: 11 residues within 4Å: Chain A: F.53, Y.72, R.74, S.135, S.184 Chain E: S.163, F.164, Y.205, C.207, C.208, Y.212 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:F.164, E:Y.205, E:Y.212, A:Y.72, A:Y.72 Hydrogen bonds: A:S.184 pi-Stacking: A:F.53

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

NAG.2: 2 residues within 4Å: Chain A: G.90, N.91 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain B: N.91 No protein-ligand interaction detected (PLIP)

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

EDO.3: 11 residues within 4Å: Chain A: T.108, A.109, A.110, S.111, S.112, F.164 Chain B: Q.55, Y.72, L.119, S.120, A.137 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.55, B:Y.72, A:S.112, A:S.112 EDO.4: 6 residues within 4Å: Chain A: D.68, R.114, Q.117, R.139, S.141 Chain E: R.114 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:D.68, E:R.114 EDO.6: 10 residues within 4Å: Chain B: T.108, A.109, A.110, S.111, S.112, F.164 Chain C: Q.55, Y.72, L.119, A.137 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.55, C:Y.72, C:Y.72, B:S.112, B:S.112 EDO.7: 8 residues within 4Å: Chain A: R.114 Chain B: D.68, R.114, P.115, Q.117, R.139, L.140, S.141 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.114, A:R.114, B:R.139, B:S.141, B:S.141 EDO.8: 4 residues within 4Å: Chain B: E.192, L.194, R.222, N.228 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.192, B:N.228 EDO.11: 10 residues within 4Å: Chain C: T.108, A.109, A.110, S.111, S.112, F.164 Chain D: Q.55, Y.72, L.119, A.137 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.55, D:Y.72, C:S.112, C:S.112 EDO.12: 7 residues within 4Å: Chain B: R.114 Chain C: R.114, P.115, Q.117, R.139, L.140, S.141 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.114, C:R.139, C:S.141 EDO.14: 11 residues within 4Å: Chain D: T.108, A.109, A.110, S.111, S.112, F.164 Chain E: Q.55, V.70, Y.72, L.119, A.137 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:S.112, D:S.112, E:Q.55, E:Y.72 EDO.15: 5 residues within 4Å: Chain C: R.114 Chain D: D.68, Q.117, R.139, S.141 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.139, D:S.141, D:S.141, C:R.114, C:R.114 Water bridges: D:D.68, D:D.68 EDO.17: 12 residues within 4Å: Chain A: Q.55, V.70, Y.72, L.119, S.120, A.137 Chain E: T.108, A.109, A.110, S.111, S.112, F.164 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:Q.55, A:Y.72, E:S.112, E:S.112 EDO.18: 5 residues within 4Å: Chain D: R.114 Chain E: D.68, P.115, R.139, S.141 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.139, E:S.141, D:R.114 EDO.19: 4 residues within 4Å: Chain E: E.192, L.194, R.222, N.228 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.192, E:R.222, E:N.228

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