SMTL ID : 4nc3.1

Crystal structure of the 5-HT2B receptor solved using serial femtosecond crystallography in lipidic cubic phase.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x PLM: PALMITIC ACID(Covalent)

PLM.1: 6 residues within 4Å: Chain A: I.36, L.37, I.41, I.411, T.412, C.413 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.36, A:L.37, A:I.41

1 x ERM: Ergotamine(Non-covalent)

ERM.2: 23 residues within 4Å: Chain A: L.107, D.110, V.111, S.114, T.115, C.182, V.183, L.184, T.185, K.186, F.192, M.193, G.196, A.200, W.353, F.356, N.360, L.363, Q.375, L.378, E.379, V.382, Y.386 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.107, A:V.111, A:V.183, A:L.184, A:F.192, A:F.356, A:L.363, A:L.378, A:E.379 Hydrogen bonds: A:T.115, A:L.184 Salt bridges: A:D.110 pi-Stacking: A:F.357

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 7 residues within 4Å: Chain A: I.36, I.41, I.44, G.45, Y.410, Y.415 Ligands: OLC.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.36, A:I.44 Hydrogen bonds: A:Y.415

4 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.4: 9 residues within 4Å: Chain A: S.125, M.208, I.209, Y.212, T.215, S.339, L.342, G.343, F.346 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.209 Hydrogen bonds: A:S.125, A:T.215 OLC.5: 2 residues within 4Å: Chain A: Y.415 Ligands: CLR.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.415 OLC.7: 3 residues within 4Å: Chain A: T.48, L.52, L.80 No protein-ligand interaction detected (PLIP) OLC.8: 6 residues within 4Å: Chain A: G.160, P.164, K.168, D.191, F.192 Ligands: OLA.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.168, A:D.191, A:D.191, A:F.192

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 4 residues within 4Å: Chain A: Y.62, N.65, Y.396, N.400 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.9: 1 residues within 4Å: Chain A: D.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.191

3 x OLA: OLEIC ACID(Non-covalent)(Non-functional Binders)

OLA.10: 1 residues within 4Å: Chain A: W.155 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.155 OLA.11: 5 residues within 4Å: Chain A: W.31, L.35, M.38, V.39, I.380 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.38, A:V.39, A:I.380 OLA.12: 1 residues within 4Å: Ligands: OLC.8 No protein-ligand interaction detected (PLIP)

2 x DGA: DIACYL GLYCEROL(Non-covalent)

DGA.13: 5 residues within 4Å: Chain A: A.206, V.210, L.214, H.217 Ligands: DGA.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.206, A:V.210, A:L.214 Salt bridges: A:H.217, A:H.217 DGA.14: 5 residues within 4Å: Chain A: F.213, I.216, H.217, Q.220 Ligands: DGA.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.213 Hydrogen bonds: A:H.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W. et al., Serial femtosecond crystallography of G protein-coupled receptors. Science (2013)

Release Date

2013-12-18

Peptides

Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562

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