SMTL ID : 2ymd.3 (2 other biounits)

Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with serotonin (5-hydroxytryptamine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-pentamer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: D.42, T.45, E.47, R.95 Chain B: K.40, R.120 Ligands: GOL.5 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.40, A:K.40, A:E.47, A:R.95, B:K.40, B:R.120, B:R.120 Water bridges: A:T.45, A:T.45 GOL.3: 6 residues within 4Å: Chain A: P.19, W.84, Y.147 Chain B: K.8, T.78, S.79 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:T.78, B:T.78 Hydrogen bonds: A:P.19, A:Y.147, A:Y.147 GOL.5: 5 residues within 4Å: Chain A: K.40, D.49, S.122 Chain E: R.95 Ligands: GOL.1 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:K.40, A:K.40, E:R.95, E:R.95 Water bridges: A:D.49, A:D.49, A:R.95 GOL.8: 6 residues within 4Å: Chain A: R.95 Chain B: K.40, D.49, R.95, R.120, S.122 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.40, B:K.40, B:R.120, B:S.122, A:R.95, A:R.95 Water bridges: B:S.122 GOL.15: 6 residues within 4Å: Chain A: K.40, R.120 Chain E: K.40, T.45, E.47, R.95 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain E Hydrogen bonds: A:K.40, A:K.40, A:R.120, A:R.120, E:K.40, E:K.40, E:E.47, E:R.95 Water bridges: E:D.42, E:D.42

5 x SRO: SEROTONIN(Non-covalent)

SRO.2: 12 residues within 4Å: Chain A: Y.91, W.145, V.146, C.188, C.189, Y.193 Chain B: W.53, I.104, V.106, M.114, F.115, I.116 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.146, A:V.146, B:V.106, B:I.116 Hydrogen bonds: A:W.145, A:Y.193, A:Y.193, B:I.104, B:I.116 Water bridges: B:I.104 SRO.6: 12 residues within 4Å: Chain B: Y.91, W.145, V.146, C.188, C.189, Y.193 Chain C: W.53, I.104, V.106, M.114, F.115, I.116 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:V.146, B:V.146, C:V.106, C:I.116 Hydrogen bonds: B:W.145, B:Y.193, B:Y.193, C:I.104, C:I.116 Water bridges: C:I.104 SRO.9: 11 residues within 4Å: Chain C: Y.91, W.145, V.146, C.188, C.189, Y.193 Chain D: I.104, V.106, M.114, F.115, I.116 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.106, D:I.116, D:I.116, C:V.146, C:V.146 Hydrogen bonds: D:I.104, D:I.116, C:Y.91, C:W.145, C:Y.193 Water bridges: D:I.104 SRO.11: 11 residues within 4Å: Chain D: Y.91, W.145, V.146, C.188, C.189, Y.193 Chain E: I.104, V.106, M.114, F.115, I.116 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:V.146, D:V.146, E:V.106, E:I.116, E:I.116 Hydrogen bonds: D:Y.91, D:Y.91, D:Y.193, E:I.104, E:I.116 pi-Stacking: D:W.145 Water bridges: E:I.104 SRO.13: 12 residues within 4Å: Chain A: W.53, I.104, V.106, M.114, F.115, I.116 Chain E: Y.91, W.145, V.146, C.188, C.189, Y.193 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:V.106, A:I.116, A:I.116, E:V.146, E:V.146 Hydrogen bonds: A:I.104, A:I.116, E:W.145, E:Y.193 Water bridges: A:I.104 pi-Stacking: E:W.145

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 7 residues within 4Å: Chain A: K.23, S.148, F.150, E.151, E.191 Chain B: D.75, R.77 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.148, A:E.151, A:E.151 Water bridges: A:E.191 Salt bridges: A:K.23, B:R.77 PO4.7: 7 residues within 4Å: Chain B: K.23, S.148, F.150, E.151, E.191 Chain C: D.75, R.77 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.148, B:E.151, B:E.151, B:E.191, B:E.191 Salt bridges: B:K.23, C:R.77 Water bridges: C:R.77 PO4.10: 6 residues within 4Å: Chain C: S.148, F.150, E.151, E.191 Chain D: D.75, R.77 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.148, C:S.148, D:D.75 Water bridges: D:R.77 Salt bridges: D:R.77 PO4.12: 6 residues within 4Å: Chain D: K.23, S.148, F.150, E.151, E.191 Chain E: R.77 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:S.148, D:E.191 Water bridges: D:K.23 Salt bridges: D:K.23, E:R.77 PO4.14: 5 residues within 4Å: Chain A: R.77 Chain E: S.148, F.150, E.151, E.191 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.148, E:S.148, E:E.191 Water bridges: A:R.77 Salt bridges: A:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kesters, D. et al., Structural Basis of Ligand Recognition in 5-Ht(3) Receptors. Embo Rep. (2013)

Release Date

2012-12-12

Peptides

SOLUBLE ACETYLCHOLINE RECEPTOR: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

SOLUBLE ACETYLCHOLINE RECEPTOR

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