SMTL ID : 2ymd.1 (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-10-mer

Ligands

10 x SRO: SEROTONIN(Non-covalent)

SRO.1: 13 residues within 4Å: Chain A: Y.91, W.145, V.146, Y.186, 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:Y.91, A:W.145, A:Y.193, B:I.104, B:I.116 Water bridges: B:I.104 SRO.5: 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 C, 5 interactions with chain B Hydrophobic interactions: C:V.106, C:I.116, B:V.146, B:V.146 Hydrogen bonds: C:I.104, C:I.116, B:W.145, B:Y.193, B:Y.193 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: W.53, I.104, V.106, F.115, I.116 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:V.146, C:V.146, D:V.106, D:I.116, D:I.116 Hydrogen bonds: C:W.145, C:Y.193, C:Y.193, D:I.104, D:I.116 pi-Stacking: C:W.145 Water bridges: D:I.104 SRO.13: 12 residues within 4Å: Chain D: Y.91, W.145, V.146, C.188, C.189, Y.193 Chain E: W.53, I.104, V.106, M.114, F.115, I.116 11 PLIP interactions: 5 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:V.106, E:I.116, D:V.146, D:V.146 Hydrogen bonds: E:I.104, E:I.116, D:Y.91, D:W.145, D:Y.193, D:Y.193 Water bridges: E:I.104 SRO.17: 12 residues within 4Å: Chain A: I.104, V.106, M.114, F.115, I.116 Chain E: Y.91, W.145, V.146, Y.186, C.188, C.189, Y.193 12 PLIP interactions: 6 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: E:V.146, E:V.146, A:V.106, A:I.116, A:I.116 Hydrogen bonds: E:Y.91, E:Y.91, E:Y.193, A:I.104, A:I.116 pi-Stacking: E:W.145 Water bridges: A:I.104 SRO.21: 12 residues within 4Å: Chain F: Y.91, W.145, V.146, C.188, C.189, Y.193 Chain G: W.53, I.104, V.106, M.114, F.115, I.116 10 PLIP interactions: 5 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: F:V.146, F:V.146, G:V.106, G:I.116 Hydrogen bonds: F:W.145, F:Y.193, F:Y.193, G:I.104, G:I.116 Water bridges: G:I.104 SRO.25: 12 residues within 4Å: Chain G: Y.91, W.145, V.146, C.188, C.189, Y.193 Chain H: W.53, I.104, V.106, M.114, F.115, I.116 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain H Hydrophobic interactions: G:V.146, G:V.146, H:V.106, H:I.116 Hydrogen bonds: G:W.145, G:Y.193, G:Y.193, H:I.104, H:I.116 Water bridges: H:I.104 SRO.28: 11 residues within 4Å: Chain H: Y.91, W.145, V.146, C.188, C.189, Y.193 Chain I: I.104, V.106, M.114, F.115, I.116 11 PLIP interactions: 5 interactions with chain H, 6 interactions with chain I Hydrophobic interactions: H:V.146, H:V.146, I:V.106, I:I.116, I:I.116 Hydrogen bonds: H:Y.91, H:W.145, H:Y.193, I:I.104, I:I.116 Water bridges: I:I.104 SRO.30: 11 residues within 4Å: Chain I: Y.91, W.145, V.146, C.188, C.189, Y.193 Chain J: I.104, V.106, M.114, F.115, I.116 12 PLIP interactions: 6 interactions with chain I, 6 interactions with chain J Hydrophobic interactions: I:V.146, I:V.146, J:V.106, J:I.116, J:I.116 Hydrogen bonds: I:Y.91, I:Y.91, I:Y.193, J:I.104, J:I.116 pi-Stacking: I:W.145 Water bridges: J:I.104 SRO.32: 12 residues within 4Å: Chain F: W.53, I.104, V.106, M.114, F.115, I.116 Chain J: Y.91, W.145, V.146, C.188, C.189, Y.193 11 PLIP interactions: 6 interactions with chain F, 5 interactions with chain J Hydrophobic interactions: F:V.106, F:I.116, F:I.116, J:V.146, J:V.146 Hydrogen bonds: F:I.104, F:I.116, J:W.145, J:Y.193 Water bridges: F:I.104 pi-Stacking: J:W.145

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: P.19, W.84, T.85, Y.147 Chain B: I.104 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:T.78 Hydrogen bonds: A:T.85, A:D.87 GOL.4: 6 residues within 4Å: Chain C: P.96, V.97 Chain D: V.99, L.100, S.101, P.102 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:V.97, D:V.99 Water bridges: C:T.89, C:S.93, C:S.93, D:Q.103 GOL.6: 5 residues within 4Å: Chain A: R.95 Chain B: K.40, D.49, S.122 Ligands: GOL.8 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.40, B:D.49, B:S.122, A:R.95, A:R.95 Water bridges: B:P.96, B:S.122 GOL.8: 6 residues within 4Å: Chain B: E.47, R.95, S.122 Chain C: K.40, R.120 Ligands: GOL.6 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.95, B:S.122, B:S.122, C:R.120, C:R.120 Water bridges: B:K.40, B:D.42, C:K.40, C:K.40 GOL.10: 6 residues within 4Å: Chain C: P.19, W.84, Y.147 Chain D: K.8, T.78, S.79 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Y.147, C:Y.147, D:S.79 Water bridges: D:T.78, D:T.78 GOL.12: 6 residues within 4Å: Chain H: P.96, V.97 Chain I: V.99, L.100, S.101, P.102 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:V.97 Water bridges: H:T.89, H:S.93 GOL.14: 5 residues within 4Å: Chain C: R.95 Chain D: K.40, D.49, R.95, S.122 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.40, D:K.40, D:R.95, D:S.122, C:R.95, C:R.95 Water bridges: D:R.95, D:R.95, D:P.96, D:R.120, D:S.122 GOL.15: 7 residues within 4Å: Chain C: T.22, D.24, D.25 Chain D: Q.1, A.2, N.3, L.4 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:T.22, C:D.24, D:Q.1, D:A.2, D:N.3, D:L.4 Water bridges: C:D.25, D:Q.1, D:N.3 GOL.18: 8 residues within 4Å: Chain A: K.8, T.78, S.79, I.104 Chain E: P.19, G.20, W.84, Y.147 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:K.8, A:S.79, E:W.84 Water bridges: A:K.8 GOL.20: 7 residues within 4Å: Chain F: D.42, T.45, E.47, R.95 Chain G: K.40, R.120 Ligands: GOL.24 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:K.40, F:K.40, F:E.47, F:R.95, G:K.40, G:R.120, G:R.120 Water bridges: F:T.45, F:T.45 GOL.22: 6 residues within 4Å: Chain F: P.19, W.84, Y.147 Chain G: K.8, T.78, S.79 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain F Water bridges: G:T.78, G:T.78 Hydrogen bonds: F:P.19, F:Y.147, F:Y.147 GOL.24: 5 residues within 4Å: Chain F: K.40, D.49, S.122 Chain J: R.95 Ligands: GOL.20 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain J Hydrogen bonds: F:K.40, F:K.40, J:R.95, J:R.95 Water bridges: F:D.49, F:D.49, F:R.95 GOL.27: 6 residues within 4Å: Chain F: R.95 Chain G: K.40, D.49, R.95, R.120, S.122 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:K.40, G:K.40, G:R.120, G:S.122, F:R.95, F:R.95 Water bridges: G:S.122 GOL.34: 6 residues within 4Å: Chain F: K.40, R.120 Chain J: K.40, T.45, E.47, R.95 10 PLIP interactions: 4 interactions with chain F, 6 interactions with chain J Hydrogen bonds: F:K.40, F:K.40, F:R.120, F:R.120, J:K.40, J:K.40, J:E.47, J:R.95 Water bridges: J:D.42, J:D.42

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

PO4.3: 7 residues within 4Å: Chain A: K.23, S.148, F.150, E.151, E.191 Chain B: D.75, R.77 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.148, B:D.75 Salt bridges: A:K.23, B:R.77 PO4.7: 5 residues within 4Å: Chain B: S.148, F.150, E.151, E.191 Chain C: R.77 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Salt bridges: C:R.77 Hydrogen bonds: B:S.148, B:E.151, B:E.151 Water bridges: B:E.151 PO4.11: 7 residues within 4Å: Chain C: K.23, S.148, F.150, E.151, E.191 Chain D: D.75, R.77 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.148, C:S.148, C:E.151 Salt bridges: C:K.23, D:R.77 PO4.16: 7 residues within 4Å: Chain D: K.23, S.148, F.150, E.151, E.191 Chain E: D.75, R.77 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:S.148, D:E.151 Water bridges: D:K.23, D:E.151, D:E.191, D:E.191, D:E.191, D:Y.193, E:R.77 Salt bridges: D:K.23, E:R.77 PO4.19: 7 residues within 4Å: Chain A: D.75, R.77 Chain E: K.23, S.148, F.150, E.151, E.191 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:E.151 Water bridges: E:K.23, E:K.23, A:D.75, A:R.77 Salt bridges: E:K.23, A:R.77 PO4.23: 7 residues within 4Å: Chain F: K.23, S.148, F.150, E.151, E.191 Chain G: D.75, R.77 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:S.148, F:E.151, F:E.151 Water bridges: F:E.191 Salt bridges: F:K.23, G:R.77 PO4.26: 7 residues within 4Å: Chain G: K.23, S.148, F.150, E.151, E.191 Chain H: D.75, R.77 8 PLIP interactions: 6 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:S.148, G:E.151, G:E.151, G:E.191, G:E.191 Salt bridges: G:K.23, H:R.77 Water bridges: H:R.77 PO4.29: 6 residues within 4Å: Chain H: S.148, F.150, E.151, E.191 Chain I: D.75, R.77 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:D.75, H:S.148, H:S.148 Water bridges: I:R.77 Salt bridges: I:R.77 PO4.31: 6 residues within 4Å: Chain I: K.23, S.148, F.150, E.151, E.191 Chain J: R.77 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:S.148, I:E.191 Water bridges: I:K.23 Salt bridges: I:K.23, J:R.77 PO4.33: 5 residues within 4Å: Chain F: R.77 Chain J: S.148, F.150, E.151, E.191 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain F Hydrogen bonds: J:S.148, J:S.148, J:E.191 Water bridges: F:R.77 Salt bridges: F: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: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

SOLUBLE ACETYLCHOLINE RECEPTOR

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