SMTL ID : 6wqa.1

2.0A angstrom A2a adenosine receptor structure using XFEL data collected in helium atmosphere.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

NA.1: 2 residues within 4Å: Chain A: D.77, S.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.116, A:N.401

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.2: 12 residues within 4Å: Chain A: L.110, F.193, E.194, M.202, W.367, L.370, H.371, N.374, H.385, L.388, M.391, I.395 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.110, A:W.367, A:L.370, A:L.388 Hydrogen bonds: A:N.374, A:N.374 Water bridges: A:K.178, A:F.193, A:H.385 Salt bridges: A:E.194 pi-Stacking: A:F.193, A:F.193

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

CLR.3: 3 residues within 4Å: Ligands: OLA.6, CLR.17, OLC.27 No protein-ligand interaction detected (PLIP) CLR.16: 7 residues within 4Å: Chain A: P.369, I.373, F.376, C.383, S.384, L.390 Ligands: OLC.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.369, A:I.373, A:F.376 Hydrogen bonds: A:S.384, A:S.384 CLR.17: 7 residues within 4Å: Chain A: A.97, A.98, G.101, I.105 Ligands: CLR.3, OLA.4, OLC.27 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.98, A:I.105, A:I.105 Hydrogen bonds: A:A.98, A:Q.188

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

OLA.4: 6 residues within 4Å: Chain A: A.98, H.100, G.101 Ligands: OLA.9, CLR.17, OLC.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.101 Water bridges: A:H.100 OLA.5: 5 residues within 4Å: Chain A: I.35, L.39, I.89 Ligands: OLA.10, OLA.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.39 OLA.6: 1 residues within 4Å: Ligands: CLR.3 No protein-ligand interaction detected (PLIP) OLA.7: 3 residues within 4Å: Chain A: S.32, I.35, T.36 No protein-ligand interaction detected (PLIP) OLA.8: 7 residues within 4Å: Chain A: G.30, S.31, Y.34, V.37, L.388, Y.392, V.396 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.34, A:V.37, A:L.388, A:Y.392, A:V.396 OLA.9: 6 residues within 4Å: Chain A: V.155, L.162, M.165, L.166 Ligands: OLA.4, OLC.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.155, A:L.162, A:L.166 OLA.10: 2 residues within 4Å: Ligands: OLA.5, OLA.12 No protein-ligand interaction detected (PLIP) OLA.12: 5 residues within 4Å: Chain A: T.90, T.93, F.95 Ligands: OLA.5, OLA.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.93, A:T.93 OLA.14: 4 residues within 4Å: Chain A: L.44, L.47, G.48, F.407 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.44, A:L.47, A:F.407 Hydrogen bonds: A:L.47 OLA.19: 6 residues within 4Å: Chain A: L.121, A.122, I.125, D.126, V.141, I.149 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.121, A:I.125, A:I.149 OLA.20: 1 residues within 4Å: Chain A: Y.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.204 OLA.21: 5 residues within 4Å: Chain A: V.71, K.147, I.150, W.154 Ligands: OLB.23 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.150, A:W.154 Salt bridges: A:K.147 OLA.22: 4 residues within 4Å: Chain A: V.50, W.54, I.78 Ligands: OLB.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.50, A:I.78 OLA.24: 4 residues within 4Å: Chain A: T.400, F.407, Y.411 Ligands: OLA.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.400, A:F.407 OLA.25: 1 residues within 4Å: Ligands: OLA.24 No protein-ligand interaction detected (PLIP)

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

OLC.11: 4 residues within 4Å: Chain A: V.155, M.165, L.166 Ligands: OLA.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.155, A:L.166 Hydrogen bonds: A:M.165 OLC.15: 5 residues within 4Å: Chain A: L.365, P.369, P.387, L.397 Ligands: CLR.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.365, A:P.369, A:L.397 OLC.18: 4 residues within 4Å: Chain A: F.205, A.209, P.214, L.217 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.205, A:P.214 OLC.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OLC.27: 3 residues within 4Å: Ligands: CLR.3, OLA.4, CLR.17 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 2 residues within 4Å: Chain A: W.54, W.57 No protein-ligand interaction detected (PLIP)

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

OLB.23: 8 residues within 4Å: Chain A: C.53, W.57, V.71, A.75, I.78, V.82 Ligands: OLA.21, OLA.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.78, A:V.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, M.-Y. et al., Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase. Iucrj (2020)

Release Date

2020-11-18

Peptides

Adenosine receptor A2a/Soluble cytochrome b562 chimera: 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 chimera

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