SMTL ID : 9fup.1

Serial microseconds crystallography at ID29 using fixed-target (small foils): A2a adenosine receptor co-crystallised with Istradefylline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: L.57, D.61, S.100, F.347, N.385 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.385 Water bridges: A:W.351

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 12 residues within 4Å: Chain A: L.67, F.71, F.79, A.81, A.82, G.85, C.86, F.88, I.89, Q.172 Ligands: OLB.17, OLC.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.79, A:A.81, A:F.88 Hydrogen bonds: A:A.82 CLR.3: 13 residues within 4Å: Chain A: L.349, L.352, P.353, I.356, I.357, F.360, C.367, S.368, H.369, A.370, P.371, L.374 Ligands: OLA.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.349, A:L.352, A:P.353, A:I.356, A:I.357, A:L.374 Hydrogen bonds: A:S.368 CLR.4: 12 residues within 4Å: Chain A: F.191, F.192, L.196, L.200, L.352, I.356, C.359, F.360, F.363, C.364 Ligands: OLA.12, OLB.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.191, A:F.192, A:L.196, A:I.356, A:F.360, A:F.360, A:F.360, A:F.363

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

OLA.5: 13 residues within 4Å: Chain A: L.23, A.26, I.30, G.65, V.66, I.69, P.70, I.73, T.74, T.77, F.79 Ligands: OLA.15, OLC.18 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.23, A:A.26, A:I.30, A:P.70, A:P.70, A:I.73, A:F.79 Hydrogen bonds: A:T.77 OLA.6: 5 residues within 4Å: Chain A: P.371, W.373, L.374, L.377 Ligands: CLR.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.371, A:L.377 OLA.7: 10 residues within 4Å: Chain A: F.53, F.102, L.105, A.106, I.109, D.110, I.113, V.125, I.133, C.137 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.106, A:I.109, A:I.109, A:I.133 Hydrogen bonds: A:D.110 OLA.8: 14 residues within 4Å: Chain A: P.11, G.14, S.15, V.17, Y.18, V.21, I.25, L.372, W.373, Y.376, L.377, V.380, T.384 Ligands: JQ9.20 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.21, A:Y.376, A:L.377, A:V.380 Hydrogen bonds: A:Y.376 OLA.9: 9 residues within 4Å: Chain A: L.28, L.31, G.32, V.34, L.35, W.38, V.387, F.391, I.408 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.28, A:L.31, A:F.391 OLA.10: 7 residues within 4Å: Chain A: L.346, L.349, C.350, L.381, T.384, V.388, I.392 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.384 OLA.11: 8 residues within 4Å: Chain A: I.30, V.34, C.37, W.38, W.41, I.62, V.66 Ligands: OLB.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.41, A:W.41 Hydrogen bonds: A:W.41 OLA.12: 11 residues within 4Å: Chain A: L.196, L.199, L.200, L.203, Y.206, A.341, A.344, G.345, A.348, L.352 Ligands: CLR.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.196, A:L.203, A:Y.206 OLA.13: 4 residues within 4Å: Chain A: S.16, I.19, T.20, L.23 No protein-ligand interaction detected (PLIP) OLA.14: 6 residues within 4Å: Chain A: H.84, V.139, L.140, A.143, M.149, L.150 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.150 Salt bridges: A:H.84 OLA.15: 2 residues within 4Å: Ligands: OLA.5, OLC.18 No protein-ligand interaction detected (PLIP)

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

OLB.16: 5 residues within 4Å: Chain A: F.192, L.196, L.200, F.363 Ligands: CLR.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.192, A:F.363, A:F.363 Hydrogen bonds: A:F.363 OLB.17: 12 residues within 4Å: Chain A: C.37, V.40, W.41, Q.47, Y.52, V.55, A.59, I.62, L.63 Ligands: CLR.2, OLA.11, OLC.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.55, A:A.59, A:L.63 Hydrogen bonds: A:Y.52

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

OLC.18: 12 residues within 4Å: Chain A: V.66, L.67, P.70, F.71, T.74, F.79, C.80, I.89, Q.172 Ligands: CLR.2, OLA.5, OLA.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.66, A:F.71, A:T.74, A:F.79, A:F.79 Hydrogen bonds: A:Q.172 OLC.19: 13 residues within 4Å: Chain A: Y.52, V.55, S.56, A.59, L.63, F.92, G.127, A.130, A.131, I.134, W.138, F.142 Ligands: OLB.17 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.55, A:L.63, A:W.138, A:W.138, A:F.142, A:F.142 Hydrogen bonds: A:Y.52, A:G.127

1 x JQ9: 8-[(~{E})-2-(3,4-dimethoxyphenyl)ethenyl]-1,3-diethyl-7-methyl-purine-2,6-dione(Non-covalent)

JQ9.20: 20 residues within 4Å: Chain A: A.72, I.75, S.76, A.90, V.93, L.94, L.176, F.177, E.178, M.183, M.186, W.351, L.354, N.358, H.369, L.372, M.375, Y.376, I.379 Ligands: OLA.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.75, A:L.94, A:F.177, A:F.177 Hydrogen bonds: A:N.358 pi-Stacking: A:F.177, A:F.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Orlans, J. et al., Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron. Commun Chem (2025)

Release Date

2025-01-22

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