SMTL ID : 6ps4.1

XFEL beta2 AR structure by ligand exchange from Timolol to ICI-118551.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x JRZ: (2S,3S)-1-[(7-methyl-2,3-dihydro-1H-inden-4-yl)oxy]-3-[(1-methylethyl)amino]butan-2-ol(Non-covalent)

JRZ.1: 14 residues within 4Å: Chain A: W.133, D.137, V.138, V.141, F.217, S.227, S.228, S.231, W.438, F.441, F.442, N.445, N.464, Y.468 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.133, A:D.137, A:V.138, A:V.141, A:F.217, A:F.441, A:F.442, A:F.442 Hydrogen bonds: A:D.137, A:N.464, A:Y.468

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

SO4.2: 7 residues within 4Å: Chain A: T.90, V.91, T.92, R.155, Y.165, Q.166, S.167 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.90, A:T.90, A:V.91, A:T.92, A:S.167 Salt bridges: A:R.155 SO4.3: 4 residues within 4Å: Chain A: F.416, K.422, K.425, R.480 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.422, A:K.425, A:R.480 SO4.4: 6 residues within 4Å: Chain A: G.366, F.367, T.368, N.369, S.370, N.385 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.367, A:N.369, A:N.369, A:S.370, A:N.385

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 7 residues within 4Å: Chain A: Y.94, T.97, S.98, C.101, I.178, W.182 Ligands: OLC.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.97, A:I.178, A:W.182, A:W.182

4 x OLA: OLEIC ACID(Non-covalent)

OLA.6: 7 residues within 4Å: Chain A: V.240, S.244, F.247, G.428, G.432, T.435 Ligands: OLC.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.240, A:V.240, A:F.247, A:T.435 OLA.7: 3 residues within 4Å: Chain A: L.108 Ligands: OLC.11, OLC.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.108 OLA.8: 4 residues within 4Å: Chain A: Y.156, F.241, V.242, R.245 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.156 Salt bridges: A:R.245 OLA.9: 7 residues within 4Å: Chain A: M.60, M.64, I.67, E.458, I.461, W.465, I.466 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.67, A:I.461, A:W.465, A:W.465, A:I.466

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

OLC.10: 4 residues within 4Å: Chain A: I.79, C.101 Ligands: CLR.5, OLC.11 No protein-ligand interaction detected (PLIP) OLC.11: 6 residues within 4Å: Chain A: I.79, A.83, L.104 Ligands: OLA.7, OLC.10, OLC.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.79, A:L.104 OLC.12: 7 residues within 4Å: Chain A: L.69, F.73, V.76, L.77, L.491 Ligands: OLA.7, OLC.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.69, A:F.73, A:V.76, A:L.77, A:L.491 OLC.13: 4 residues within 4Å: Chain A: W.146, I.177, V.184 Ligands: OLC.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.146, A:W.146, A:I.177, A:I.177, A:V.184 OLC.14: 8 residues within 4Å: Chain A: W.146, V.150, V.153, D.154, F.157, L.168, L.169 Ligands: OLC.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.146, A:V.150 Water bridges: A:L.168 OLC.15: 8 residues within 4Å: Chain A: F.247, F.416, K.425, G.428, I.429, G.432, L.436 Ligands: OLA.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.436 OLC.16: 7 residues within 4Å: Chain A: L.77, C.479, R.485, F.488, Q.489, L.492, L.494 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.77, A:F.488, A:F.488, A:L.492 OLC.17: 1 residues within 4Å: Chain A: L.492 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.492 OLC.18: 3 residues within 4Å: Chain A: F.113, F.125, W.129 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.113, A:W.129 OLC.19: 3 residues within 4Å: Chain A: S.65, L.119, M.120 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishchenko, A. et al., Toward G protein-coupled receptor structure-based drug design using X-ray lasers. Iucrj (2019)

Release Date

2019-11-13

Peptides

Fusion protein of Beta-2 adrenergic receptor and T4 Lysozyme: 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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Fusion protein of Beta-2 adrenergic receptor and T4 Lysozyme

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