SMTL ID : 5k2b.1

2.5 angstrom A2a adenosine receptor structure with MR phasing using XFEL data

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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.1: 10 residues within 4Å: Chain A: L.110, F.193, E.194, W.367, L.370, H.371, N.374, L.388, M.391, I.395 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.110, A:W.367, A:L.388 Hydrogen bonds: A:N.374, A:N.374 Water bridges: A:F.193, A:Y.392 Salt bridges: A:E.194 pi-Stacking: A:F.193, A:F.193

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

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

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 6 residues within 4Å: Chain A: C.375, F.376, F.379, C.380 Ligands: OLC.7, OLC.21 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.376, A:F.376, A:F.376, A:F.379 Water bridges: A:F.379 CLR.4: 7 residues within 4Å: Chain A: P.369, I.373, F.376, C.383, S.384, L.390 Ligands: OLC.21 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.369, A:I.373, A:F.376, A:L.390 Hydrogen bonds: A:S.384 Water bridges: A:S.384 CLR.5: 6 residues within 4Å: Chain A: A.97, A.98, G.101, I.105 Ligands: OLB.6, OLC.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.97, A:A.98, A:I.105 Hydrogen bonds: A:A.98

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

OLB.6: 5 residues within 4Å: Chain A: L.83, T.90, F.95, C.96 Ligands: CLR.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.83, A:T.90 Hydrogen bonds: A:C.96, A:C.96

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

OLC.7: 3 residues within 4Å: Chain A: F.379, P.381 Ligands: CLR.3 No protein-ligand interaction detected (PLIP) OLC.8: 6 residues within 4Å: Chain A: C.53, W.57, V.71, A.75, I.78 Ligands: OLC.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.71, A:A.75, A:I.78 OLC.9: 7 residues within 4Å: Chain A: Y.68, S.72, A.75, K.147, I.150, W.154 Ligands: OLC.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.154, A:W.154 Hydrogen bonds: A:S.72, A:K.147 OLC.10: 4 residues within 4Å: Chain A: H.100, A.159, M.165, L.166 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.159, A:L.166 Hydrogen bonds: A:M.165 OLC.11: 1 residues within 4Å: Ligands: OLA.17 No protein-ligand interaction detected (PLIP) OLC.12: 8 residues within 4Å: Chain A: P.27, G.30, S.31, Y.34, L.388, Y.392 Ligands: OLA.14, OLA.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.34, A:Y.392 OLC.20: 4 residues within 4Å: Chain A: I.89, T.90, T.93 Ligands: OLA.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.89 Hydrogen bonds: A:T.93, A:T.93 OLC.21: 4 residues within 4Å: Chain A: F.376, C.383 Ligands: CLR.3, CLR.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.376 OLC.22: 4 residues within 4Å: Chain A: H.100, G.101, M.165 Ligands: CLR.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.100

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

OLA.13: 4 residues within 4Å: Chain A: L.44, L.47, G.48, W.54 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.44 OLA.14: 2 residues within 4Å: Chain A: W.389 Ligands: OLC.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.389, A:W.389 OLA.15: 2 residues within 4Å: Chain A: W.389 Ligands: OLC.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.389 OLA.16: 5 residues within 4Å: Chain A: A.122, I.125, D.126, V.141, I.149 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.122, A:I.125, A:I.149 OLA.17: 4 residues within 4Å: Chain A: I.35, L.39 Ligands: OLC.11, OLC.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.35, A:L.39 OLA.18: 1 residues within 4Å: Chain A: T.36 No protein-ligand interaction detected (PLIP) OLA.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OLA.23: 3 residues within 4Å: Chain A: G.361, L.362, L.365 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Batyuk, A. et al., Native phasing of x-ray free-electron laser data for a G protein-coupled receptor. Sci Adv (2016)

Release Date

2016-09-21

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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