SMTL ID : 2y57.1

Fragment growing induces conformational changes in acetylcholine- binding protein: A structural and thermodynamic analysis - (Compound 4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-pentamer

Ligands

5 x V37: [(1R,5S)-8-PHENETHYL-8-AZABICYCLO[3.2.1]OCTAN-3-YL] BENZOATE(Non-covalent)

V37.1: 15 residues within 4Å: Chain A: T.89, Y.91, K.141, F.142, G.143, S.144, W.145, Y.186, C.188, C.189, Y.193, D.195 Chain B: Y.53, Q.55, I.116 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:Q.55, B:I.116, B:I.116, A:Y.91, A:Y.91, A:K.141, A:W.145, A:W.145, A:Y.186, A:Y.193, A:Y.193, A:D.195 V37.5: 15 residues within 4Å: Chain B: T.89, Y.91, K.141, G.143, S.144, W.145, Y.186, C.188, C.189, Y.193, D.195 Chain C: Y.53, Q.55, M.114, I.116 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:Y.91, B:K.141, B:W.145, B:W.145, B:Y.186, B:Y.193, B:Y.193, B:D.195, C:Y.53, C:Q.55, C:I.116, C:I.116, C:I.116 pi-Stacking: B:Y.91 V37.9: 15 residues within 4Å: Chain C: T.89, Y.91, K.141, G.143, S.144, W.145, Y.186, C.188, C.189, Y.193, D.195 Chain D: Y.53, Q.55, M.114, I.116 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Y.91, C:Y.91, C:K.141, C:W.145, C:Y.186, C:Y.193, C:D.195, D:Y.53, D:Q.55, D:I.116, D:I.116 V37.12: 15 residues within 4Å: Chain D: T.89, Y.91, K.141, F.142, G.143, S.144, W.145, Y.186, C.188, C.189, Y.193, D.195 Chain E: Y.53, Q.55, I.116 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:Y.91, D:Y.91, D:K.141, D:W.145, D:W.145, D:Y.186, D:Y.193, D:Y.193, D:D.195, E:Q.55, E:Q.55, E:I.116 V37.15: 16 residues within 4Å: Chain A: Y.53, Q.55, M.114, I.116 Chain E: T.89, Y.91, K.141, F.142, G.143, S.144, W.145, Y.186, C.188, C.189, Y.193, D.195 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain E Hydrophobic interactions: A:Y.53, A:Q.55, A:Q.55, A:I.116, A:I.116, E:Y.91, E:Y.91, E:K.141, E:W.145, E:W.145, E:Y.186, E:Y.186, E:Y.193, E:Y.193, E:D.195

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

CL.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain C: K.40 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain D: K.40 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: K.141, Q.182, Q.184, N.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.182, A:Q.182, A:N.197 Salt bridges: A:K.141 SO4.4: 4 residues within 4Å: Chain A: Y.167, S.169 Chain E: D.126, T.137 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:D.126, E:T.137, A:S.169 SO4.7: 2 residues within 4Å: Chain B: V.183, H.185 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.185 SO4.8: 2 residues within 4Å: Chain B: P.102, Q.103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.103 SO4.11: 2 residues within 4Å: Chain C: P.102, Q.103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.103 SO4.14: 4 residues within 4Å: Chain D: K.141, Q.182, Q.184, N.197 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.182, D:N.197 Salt bridges: D:K.141 SO4.17: 4 residues within 4Å: Chain D: D.126, T.137 Chain E: Y.167, S.169 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:S.169, D:D.126, D:T.137 SO4.18: 4 residues within 4Å: Chain E: K.141, Q.182, Q.184, N.197 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.182, E:N.197 Salt bridges: E:K.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edink, E. et al., Fragment Growing Induces Conformational Changes in Acetylcholine-Binding Protein: A Structural and Thermodynamic Analysis. J.Am.Chem.Soc. (2011)

Release Date

2011-06-15

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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