SMTL ID : 6ps2.1

XFEL beta2 AR structure by ligand exchange from Timolol to Alprenolol.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x JTZ: (2S)-1-[(1-methylethyl)amino]-3-(2-prop-2-en-1-ylphenoxy)propan-2-ol(Non-covalent)

JTZ.1: 14 residues within 4Å: Chain A: W.133, T.134, D.137, V.138, V.141, T.142, F.217, S.227, S.231, W.438, F.441, F.442, N.445, N.464 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.133, A:T.134, A:V.138, A:F.217, A:F.217 Hydrogen bonds: A:N.464, A:N.464, A:N.464, A:Y.468 pi-Stacking: A:F.442

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 8 residues within 4Å: Chain A: Y.94, T.97, S.98, C.101, I.178, L.179, W.182 Ligands: OLC.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.97, A:I.178, A:I.178, A:L.179, A:W.182, A:W.182, A:W.182

7 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.3: 6 residues within 4Å: Chain A: I.79, A.83, K.84 Ligands: OLC.15, OLC.16, OLA.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.79 OLB.4: 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 OLB.5: 7 residues within 4Å: Chain A: W.146, V.150, V.153, D.154, F.157, L.168, L.169 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.146 Water bridges: A:S.167, A:L.168 OLB.6: 6 residues within 4Å: Chain A: K.425, G.428, I.429, G.432, T.433 Ligands: OLA.20 No protein-ligand interaction detected (PLIP) OLB.7: 2 residues within 4Å: Chain A: L.492 Ligands: OLC.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.492 OLB.8: 6 residues within 4Å: Chain A: L.77, C.479, R.485, F.488, L.492, L.494 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.488, A:L.492 OLB.10: 2 residues within 4Å: Chain A: S.65, L.119 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.119

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

OLC.9: 5 residues within 4Å: Chain A: W.146, I.177, M.180, V.181, V.184 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.146, A:W.146, A:I.177, A:M.180, A:V.181, A:V.184 OLC.15: 6 residues within 4Å: Chain A: I.79, T.97, C.101, L.104 Ligands: CLR.2, OLB.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.104 Hydrogen bonds: A:Y.94, A:Y.94 OLC.16: 6 residues within 4Å: Chain A: F.73, L.77, L.491 Ligands: OLB.3, OLB.7, OLA.18 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.73, A:F.73, A:F.73, A:F.73, A:L.77

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

SO4.11: 7 residues within 4Å: Chain A: T.90, V.91, T.92, R.155, Y.165, Q.166, S.167 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.90, A:V.91, A:T.92, A:T.92, A:Y.165, A:S.167 Salt bridges: A:R.155 SO4.12: 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 SO4.13: 5 residues within 4Å: Chain A: F.367, T.368, N.369, S.370, N.385 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.367, A:N.369, A:S.370, A:N.385 SO4.14: 4 residues within 4Å: Chain A: T.395, P.396, N.397, R.398 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.395, A:N.397, A:N.397, A:R.398

4 x OLA: OLEIC ACID(Non-covalent)

OLA.17: 6 residues within 4Å: Chain A: M.60, M.64, I.118, I.461, W.465, I.466 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.118, A:I.461, A:W.465, A:W.465, A:I.466 OLA.18: 3 residues within 4Å: Chain A: T.80 Ligands: OLB.3, OLC.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.80 OLA.19: 4 residues within 4Å: Chain A: Y.156, F.241, V.242, R.245 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.156, A:Y.156, A:F.241, A:V.242 Hydrogen bonds: A:F.241 Salt bridges: A:R.245 OLA.20: 7 residues within 4Å: Chain A: V.240, S.244, F.247, G.428, G.432, T.435 Ligands: OLB.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.247, A:T.435

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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