SMTL ID : 6zdv.1

Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with Chromone 5d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

monomer

Ligands

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

QGW.1: 14 residues within 4Å: Chain A: Y.18, A.72, I.75, S.76, L.94, L.176, F.177, M.186, W.351, L.354, H.355, N.358, Y.376, I.379 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.72, A:I.75, A:L.176, A:F.177, A:L.354, A:Y.376, A:I.379 Hydrogen bonds: A:F.177, A:N.358 Water bridges: A:E.178 pi-Stacking: A:F.177

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

NA.2: 4 residues within 4Å: Chain A: L.57, D.61, S.100, N.385 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.61, A:S.100, A:N.385 Water bridges: A:D.61, A:N.389

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, L.374 Ligands: OLA.10, OLA.17 7 PLIP interactions: 7 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 Water bridges: A:S.368 CLR.4: 2 residues within 4Å: Ligands: CLR.5, OLB.6 No protein-ligand interaction detected (PLIP) CLR.5: 10 residues within 4Å: Chain A: L.352, I.356, C.359, F.360, F.363, C.364 Ligands: CLR.4, OLB.6, OLA.15, OLA.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.352, A:I.356, A:F.360, A:F.360, A:F.360, A:F.363, A:F.363

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

OLB.6: 3 residues within 4Å: Chain A: F.363 Ligands: CLR.4, CLR.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.363

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

OLA.7: 6 residues within 4Å: Chain A: C.37, V.40, W.41, V.55, A.59 Ligands: OLA.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.41, A:V.55, A:A.59 Hydrogen bonds: A:W.41 OLA.8: 2 residues within 4Å: Ligands: OLA.15, OLA.17 No protein-ligand interaction detected (PLIP) OLA.9: 1 residues within 4Å: Chain A: W.138 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.138 OLA.10: 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.11: 2 residues within 4Å: Chain A: V.387, V.388 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.387, A:V.388 OLA.12: 2 residues within 4Å: Chain A: S.16, T.20 No protein-ligand interaction detected (PLIP) OLA.13: 1 residues within 4Å: Ligands: OLA.7 No protein-ligand interaction detected (PLIP) OLA.14: 3 residues within 4Å: Chain A: A.106, I.109, I.133 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.109, A:I.109, A:I.133 OLA.15: 3 residues within 4Å: Ligands: CLR.5, OLA.8, OLA.17 No protein-ligand interaction detected (PLIP) OLA.16: 3 residues within 4Å: Chain A: G.14, V.21, Y.376 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.21, A:Y.376 Hydrogen bonds: A:G.14 OLA.17: 7 residues within 4Å: Chain A: F.360, D.366, C.367 Ligands: CLR.3, CLR.5, OLA.8, OLA.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.360 OLA.18: 1 residues within 4Å: Chain A: Y.188 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.188, A:Y.188, A:Y.188 OLA.19: 1 residues within 4Å: Chain A: L.199 No protein-ligand interaction detected (PLIP) OLA.20: 1 residues within 4Å: Chain A: G.345 No protein-ligand interaction detected (PLIP)

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

OLC.21: 6 residues within 4Å: Chain A: Y.52, V.55, A.59, G.127, A.131, W.138 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.59, 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.
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Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a

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