SMTL ID : 6ps7.1

XFEL A2aR structure by ligand exchange from LUF5843 to ZM241385.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ZMA: 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol(Non-covalent)

ZMA.1: 11 residues within 4Å: Chain A: L.105, F.188, E.189, M.197, W.362, L.365, H.366, N.369, H.380, M.386, I.390 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.105, A:W.362, A:L.365 Hydrogen bonds: A:N.369, A:N.369 Water bridges: A:F.188 Salt bridges: A:E.189 pi-Stacking: A:F.188, A:F.188

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

OLC.2: 8 residues within 4Å: Chain A: C.48, V.51, W.52, V.66, A.70, I.73 Ligands: OLC.3, OLA.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.70, A:I.73 OLC.3: 8 residues within 4Å: Chain A: Y.63, V.66, A.70, K.142, I.145, W.149 Ligands: OLC.2, OLA.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.70, A:W.149 OLC.4: 7 residues within 4Å: Chain A: G.25, S.26, Y.29, L.383, W.384, Y.387 Ligands: OLA.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.29 Water bridges: A:S.26, A:S.26, A:S.87, A:S.87 OLC.5: 4 residues within 4Å: Chain A: F.371, C.378 Ligands: CLR.11, CLR.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.371 OLC.6: 3 residues within 4Å: Chain A: F.374 Ligands: OLC.10, CLR.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.374 Water bridges: A:F.373, A:F.374 OLC.7: 3 residues within 4Å: Chain A: G.96, M.160 Ligands: CLR.13 No protein-ligand interaction detected (PLIP) OLC.8: 1 residues within 4Å: Ligands: OLA.22 No protein-ligand interaction detected (PLIP) OLC.9: 5 residues within 4Å: Chain A: L.210, L.214, A.352, V.355 Ligands: CLR.11 No protein-ligand interaction detected (PLIP) OLC.10: 3 residues within 4Å: Chain A: Y.199, F.203 Ligands: OLC.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.203

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.11: 7 residues within 4Å: Chain A: C.370, F.371, F.374, C.375 Ligands: OLC.5, OLC.6, OLC.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.371, A:F.371, A:F.371, A:F.374 Water bridges: A:F.374 CLR.12: 7 residues within 4Å: Chain A: L.360, P.364, I.368, F.371, C.378, S.379 Ligands: OLC.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.360, A:P.364, A:I.368, A:F.371 Hydrogen bonds: A:S.379 Water bridges: A:S.379 CLR.13: 6 residues within 4Å: Chain A: L.78, A.92, A.93, G.96, I.100 Ligands: OLC.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.78, A:I.100, A:I.100 Hydrogen bonds: A:A.93

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

OLB.14: 3 residues within 4Å: Chain A: A.154, M.160, L.161 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.154, A:L.161

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

OLA.15: 2 residues within 4Å: Ligands: OLC.4, OLA.21 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.384, A:W.384 OLA.16: 4 residues within 4Å: Chain A: F.64, A.117, I.120, V.136 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.120, A:I.120 OLA.17: 2 residues within 4Å: Chain A: S.27, T.31 No protein-ligand interaction detected (PLIP) OLA.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OLA.19: 5 residues within 4Å: Chain A: L.39, L.42, G.43, W.49, F.402 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.402 OLA.20: 1 residues within 4Å: Chain A: I.353 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.353 OLA.21: 2 residues within 4Å: Chain A: W.384 Ligands: OLA.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.384, A:W.384 OLA.22: 4 residues within 4Å: Chain A: I.30, L.34 Ligands: OLC.8, OLA.26 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.34 OLA.23: 3 residues within 4Å: Chain A: C.48 Ligands: OLC.2, OLA.24 No protein-ligand interaction detected (PLIP) OLA.24: 2 residues within 4Å: Chain A: W.52 Ligands: OLA.23 No protein-ligand interaction detected (PLIP) OLA.25: 3 residues within 4Å: Chain A: I.145, F.153 Ligands: OLC.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.153 OLA.26: 5 residues within 4Å: Chain A: I.84, T.85, T.88, F.90 Ligands: OLA.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.84 Hydrogen bonds: A:T.88, A:T.88 OLA.27: 4 residues within 4Å: Chain A: P.81, T.85, F.90, C.91 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.81, A:T.85, A:F.90 Hydrogen bonds: A:C.91 Water bridges: A:C.91

1 x NA: SODIUM ION(Non-functional Binders)

NA.28: 3 residues within 4Å: Chain A: D.72, S.111, N.396 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.72, A:S.111

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

Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a: 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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Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a