SMTL ID : 6zdr.1

Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with Chromone 4d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x QGE: [3-(4-methyl-1,3-thiazol-2-yl)-4-oxidanylidene-6-propyl-chromen-7-yl] ethanoate(Non-covalent)

QGE.1: 13 residues within 4Å: Chain A: L.94, F.177, E.178, M.186, W.351, L.354, H.355, N.358, H.369, L.372, M.375, Y.376, I.379 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.177, A:E.178, A:L.372, A:Y.376, A:I.379 Hydrogen bonds: A:N.358 Salt bridges: A:H.369 pi-Stacking: A:F.177

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

NA.2: 3 residues within 4Å: Chain A: D.61, S.100, N.385 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.61, A:S.100, A:N.385

3 x CLR: CHOLESTEROL(Non-covalent)(Non-functional Binders)

CLR.3: 9 residues within 4Å: Chain A: L.352, P.353, I.357, F.360, C.367, S.368, A.370, L.374 Ligands: OLA.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.352, A:P.353, A:I.357, A:F.360, A:L.374 Hydrogen bonds: A:S.368 CLR.4: 9 residues within 4Å: Chain A: F.191, L.352, I.356, C.359, F.360, F.363, C.364 Ligands: CLR.5, OLC.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.191, A:L.352, A:I.356, A:F.360, A:F.360, A:F.360, A:F.363, A:F.363 CLR.5: 2 residues within 4Å: Ligands: CLR.4, OLC.11 No protein-ligand interaction detected (PLIP)

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

OLA.6: 2 residues within 4Å: Chain A: P.371 Ligands: CLR.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.371 OLA.7: 4 residues within 4Å: Chain A: L.28, L.31, G.32, F.391 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.28, A:L.31, A:F.391, A:F.391 OLA.8: 4 residues within 4Å: Chain A: S.15, I.19, L.23, T.77 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.23, A:T.77 Hydrogen bonds: A:S.15 OLA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OLA.10: 5 residues within 4Å: Chain A: L.199, Y.206, A.341, A.344, A.348 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.206, A:A.344, A:A.348 OLA.14: 3 residues within 4Å: Chain A: M.149, L.150 Ligands: OLA.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.149 Water bridges: A:H.84 Salt bridges: A:H.84 OLA.15: 7 residues within 4Å: Chain A: V.139, F.142, A.143, L.146, M.149, L.150 Ligands: OLA.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.139, A:F.142, A:F.142, A:L.146 OLA.17: 6 residues within 4Å: Chain A: P.70, T.74, T.77, F.79 Ligands: OLC.12, OLC.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.77, A:F.79 Hydrogen bonds: A:T.77 OLA.18: 6 residues within 4Å: Chain A: G.14, V.17, W.373, Y.376, L.377, V.380 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.17, A:W.373, A:Y.376, A:L.377, A:V.380 Water bridges: A:S.15, A:W.373 OLA.19: 5 residues within 4Å: Chain A: C.37, V.40, W.41, V.55, A.59 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.41, A:V.55, A:A.59 OLA.20: 7 residues within 4Å: Chain A: F.53, F.102, L.105, I.109, D.110, V.125, I.133 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.53, A:L.105, A:I.109, A:V.125, A:I.133, A:I.133

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

OLC.11: 4 residues within 4Å: Chain A: L.196, F.363 Ligands: CLR.4, CLR.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.363 Water bridges: A:F.363 OLC.12: 4 residues within 4Å: Chain A: A.26, G.65 Ligands: OLC.13, OLA.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.26 OLC.13: 7 residues within 4Å: Chain A: L.67, T.74, F.79, C.80, Q.172 Ligands: OLC.12, OLA.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.67, A:F.79 Hydrogen bonds: A:C.80, A:Q.172 Water bridges: A:C.80 OLC.16: 9 residues within 4Å: Chain A: Y.52, V.55, L.63, L.67, F.88, F.92, G.127, I.134, W.138 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.63, A:F.88, A:F.92, A:W.138, A:W.138 Hydrogen bonds: A:G.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jespers, W. et al., X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A 2A Adenosine Receptor Antagonists. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2020-09-16

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.
Show / Hide

Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a

Related Entries With Identical Sequence