SMTL ID : 8rwh.1

Dark structure of the human adenosine A2A receptor bound to synthetic photoswitch 'StilSwitch2' determined by serial synchrotron crystallography

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

1 x 01: 8-[(~{E})-2-[3,4-bis(oxidanyl)phenyl]ethenyl]-1,3-diethyl-7-methyl-purine-2,6-dione

01.1: 13 residues within 4Å: Chain A: A.88, V.109, L.110, F.193, E.194, M.202, W.367, L.370, N.374, H.385, L.388, M.391, I.395 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.88, A:E.194, A:W.367, A:L.370, A:I.395 Hydrogen bonds: A:N.374 pi-Stacking: A:F.193, A:F.193

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 6 residues within 4Å: Chain A: A.97, A.98, G.101, I.105 Ligands: OLA.25, OLA.26 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.97, A:I.105 Hydrogen bonds: A:A.98, A:Q.188 CLR.3: 7 residues within 4Å: Chain A: L.368, P.369, I.373, C.383, S.384, L.390 Ligands: OLA.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.368, A:P.369, A:I.373, A:L.390 Hydrogen bonds: A:S.384 CLR.4: 6 residues within 4Å: Chain A: C.375, F.376, F.379, C.380 Ligands: OLA.15, OLB.23 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.376, A:F.376, A:F.379, A:F.379

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

OLA.5: 6 residues within 4Å: Chain A: T.90, T.93, F.95 Ligands: OLA.10, OLA.21, OLA.25 Ligand excluded by PLIP OLA.6: 2 residues within 4Å: Chain A: P.387 Ligands: CLR.3 Ligand excluded by PLIP OLA.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OLA.8: 3 residues within 4Å: Chain A: F.69, A.122, V.141 Ligand excluded by PLIP OLA.9: 5 residues within 4Å: Chain A: G.30, W.389, Y.392, L.393, V.396 Ligand excluded by PLIP OLA.10: 3 residues within 4Å: Ligands: OLA.5, OLA.20, OLA.21 Ligand excluded by PLIP OLA.11: 4 residues within 4Å: Chain A: L.44, L.47, G.48, F.407 Ligand excluded by PLIP OLA.12: 1 residues within 4Å: Chain A: W.389 Ligand excluded by PLIP OLA.13: 1 residues within 4Å: Ligands: OLA.22 Ligand excluded by PLIP OLA.14: 3 residues within 4Å: Chain A: V.50, W.57 Ligands: OLA.28 Ligand excluded by PLIP OLA.15: 6 residues within 4Å: Chain A: L.215, A.357, A.360, G.361, A.364 Ligands: CLR.4 Ligand excluded by PLIP OLA.16: 3 residues within 4Å: Chain A: S.32, T.36, L.39 Ligand excluded by PLIP OLA.17: 4 residues within 4Å: Chain A: M.165, L.166 Ligands: OLA.18, OLA.27 Ligand excluded by PLIP OLA.18: 5 residues within 4Å: Chain A: H.100, M.165, L.166 Ligands: OLA.17, OLA.26 Ligand excluded by PLIP OLA.19: 3 residues within 4Å: Chain A: A.151, F.158 Ligands: OLC.24 Ligand excluded by PLIP OLA.20: 2 residues within 4Å: Ligands: OLA.10, OLA.25 Ligand excluded by PLIP OLA.21: 5 residues within 4Å: Chain A: I.28, S.31, T.93 Ligands: OLA.5, OLA.10 Ligand excluded by PLIP OLA.22: 3 residues within 4Å: Chain A: I.41, V.403 Ligands: OLA.13 Ligand excluded by PLIP OLA.25: 6 residues within 4Å: Chain A: L.83, T.90, F.95 Ligands: CLR.2, OLA.5, OLA.20 Ligand excluded by PLIP OLA.26: 2 residues within 4Å: Ligands: CLR.2, OLA.18 Ligand excluded by PLIP OLA.27: 1 residues within 4Å: Ligands: OLA.17 Ligand excluded by PLIP OLA.28: 4 residues within 4Å: Chain A: V.56, W.57, V.71 Ligands: OLA.14 Ligand excluded by PLIP

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

OLB.23: 2 residues within 4Å: Chain A: F.379 Ligands: CLR.4 No protein-ligand interaction detected (PLIP)

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

OLC.24: 8 residues within 4Å: Chain A: Y.68, A.75, L.79, G.143, I.150, W.154, F.158 Ligands: OLA.19 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.75, A:L.79, A:W.154, A:F.158 Hydrogen bonds: A:G.143

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

NA.29: 3 residues within 4Å: Chain A: D.77, S.116, N.401 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.116, A:S.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glover, H. et al., Photoswitch dissociation from a G protein-coupled receptor resolved by time-resolved serial crystallography. Nat Commun (2024)

Release Date

2025-01-08

Peptides

Adenosine receptor A2a,Soluble cytochrome b562: 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

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