SMTL ID : 2y58.1

Fragment growing induces conformational changes in acetylcholine- binding protein: A structural and thermodynamic analysis - (Compound 6)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-pentamer

Ligands

5 x V38: [(1R,5S)-8-[(2R)-2-HYDROXY-2-PHENYL-ETHYL]-8-METHYL-8-AZONIABICYCLO[3.2.1]OCTAN-3-YL] BENZOATE(Non-covalent)

V38.1: 13 residues within 4Å: Chain A: Y.91, S.144, W.145, V.146, Y.186, C.188, C.189, Y.193 Chain B: Q.36, Y.53, V.106, M.114, I.116 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Q.36, B:Y.53, B:V.106, B:I.116, A:Y.91, A:W.145, A:Y.186, A:Y.193, A:Y.193 Hydrogen bonds: B:Y.53 pi-Cation interactions: A:Y.91, A:Y.186 V38.5: 12 residues within 4Å: Chain B: Y.91, W.145, Y.186, C.188, C.189, Y.193 Chain C: Q.36, Y.53, V.106, M.114, I.116, S.165 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:Q.36, C:V.106, C:I.116, B:Y.91, B:W.145, B:W.145, B:W.145, B:Y.193 pi-Stacking: C:Y.53 Hydrogen bonds: B:Y.186 pi-Cation interactions: B:Y.91, B:W.145, B:Y.186 V38.9: 9 residues within 4Å: Chain C: Y.91, W.145, Y.186, C.188, Y.193 Chain D: Q.36, Y.53, M.114, I.116 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.91, C:Y.91, C:W.145, C:Y.186, C:Y.186, C:Y.193, D:I.116 pi-Cation interactions: C:Y.91, C:Y.186 Hydrogen bonds: D:S.165 V38.11: 11 residues within 4Å: Chain D: Y.91, W.145, Y.186, C.188, C.189, Y.193 Chain E: Q.36, Y.53, V.106, M.114, I.116 13 PLIP interactions: 8 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:Y.91, D:Y.91, D:W.145, D:Y.186, D:Y.193, E:Q.36, E:Y.53, E:V.106, E:I.116 pi-Cation interactions: D:Y.91, D:W.145, D:Y.186 Hydrogen bonds: E:Y.53 V38.13: 13 residues within 4Å: Chain A: Q.36, Y.53, V.106, M.114, I.116 Chain E: Y.91, S.144, W.145, V.146, Y.186, C.188, C.189, Y.193 12 PLIP interactions: 7 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:Y.91, E:W.145, E:Y.186, E:Y.193, E:Y.193, A:Q.36, A:Y.53, A:V.106, A:I.116 pi-Cation interactions: E:Y.91, E:Y.186 Hydrogen bonds: A:Y.53

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

CL.2: 2 residues within 4Å: Chain A: R.95 Chain B: K.40 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain C: K.40 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: D.126 Chain B: Y.167, S.169 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain D: K.40 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain D: R.95 Chain E: K.40 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: K.40 Ligand excluded by PLIP

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

SO4.3: 4 residues within 4Å: Chain A: Y.167, S.169 Chain E: C.125, D.126 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Y.167, A:S.169, A:S.169, E:D.126 SO4.4: 2 residues within 4Å: Chain A: P.102, Q.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.103 SO4.8: 4 residues within 4Å: Chain C: C.125, D.126 Chain D: Y.167, S.169 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.169, D:S.169, C:D.126 SO4.15: 4 residues within 4Å: Chain E: K.141, Q.182, Q.184, N.197 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.184 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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