SMTL ID : 4pir.1

X-ray structure of the mouse serotonin 5-HT3 receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-5-5-mer

Ligands

9 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: D.81, N.82 Chain B: R.34 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.148, F.193, Q.195, K.197, Y.213, I.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.197, A:Y.213 NAG-NAG.5: 3 residues within 4Å: Chain B: D.81, N.82 Chain C: R.34 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: N.148, F.193, K.197, Y.213, I.215 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.197 NAG-NAG.8: 3 residues within 4Å: Chain C: D.81, N.82 Chain D: R.34 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: N.148, F.193, K.197, Y.213, I.215 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.197, C:Y.213 NAG-NAG.11: 3 residues within 4Å: Chain D: D.81, N.82 Chain E: R.34 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain D: N.148, F.193, Q.195, K.197, Y.213, I.215 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.195, D:K.197, D:Y.213 NAG-NAG.14: 7 residues within 4Å: Chain E: N.148, E.191, F.193, Q.195, K.197, Y.213, I.215 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.195, E:K.197, E:Y.213

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)(Post Translational Modification)

NAG-NAG-BMA.2: 3 residues within 4Å: Chain A: N.164, T.166, F.196 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.196 NAG-NAG-BMA.4: 5 residues within 4Å: Chain B: I.160, N.164, I.165, T.166, F.196 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.196 NAG-NAG-BMA.7: 3 residues within 4Å: Chain C: N.164, T.166, F.196 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.196 NAG-NAG-BMA.10: 3 residues within 4Å: Chain D: N.164, T.166, F.196 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.196 NAG-NAG-BMA.13: 3 residues within 4Å: Chain E: N.164, T.166, F.196 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.196

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

CL.15: 2 residues within 4Å: Chain A: R.31, K.35 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: R.31, K.35 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: R.31, K.35 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain D: R.31, K.35 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain E: R.31, K.35 Ligand excluded by PLIP

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

SO4.18: 0 residues within 4Å: (No contacts) 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain E Salt bridges: C:K.108, A:K.108, B:K.108, D:K.108, E:K.108 SO4.23: 3 residues within 4Å: Chain H: R.19, K.80, Y.84 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Y.84, H:Y.84 Salt bridges: H:R.19, H:K.80 SO4.24: 2 residues within 4Å: Chain H: P.14, S.124 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:S.124, H:S.124

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

NAG.20: 1 residues within 4Å: Ligands: NAG.21 No protein-ligand interaction detected (PLIP) NAG.21: 4 residues within 4Å: Chain A: R.34 Chain E: D.81, N.82 Ligands: NAG.20 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.82, A:R.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hassaine, G. et al., X-ray structure of the mouse serotonin 5-HT3 receptor. Nature (2014)

Release Date

2014-08-06

Peptides

5-hydroxytryptamine receptor 3A: ABCDE
VHH15: FGHIJ

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

Membrane

We predict this structure to be a membrane protein.
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5-hydroxytryptamine receptor 3A

VHH15