SMTL ID : 5k2c.1

1.9 angstrom A2a adenosine receptor structure with sulfur SAD phasing and phase extension using XFEL data

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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: 11 residues within 4Å: Chain A: L.110, F.193, E.194, M.202, W.367, L.370, H.371, N.374, H.385, M.391, I.395 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.110, A:W.367, A:M.391 Hydrogen bonds: A:N.374, A:N.374 Water bridges: A:F.193 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:S.116, A:S.116, A:N.401

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 7 residues within 4Å: Chain A: A.97, A.98, G.101, I.105 Ligands: OLC.6, OLC.7, OLC.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.105 Hydrogen bonds: A:A.98 CLR.4: 9 residues within 4Å: Chain A: L.365, L.368, P.369, I.373, F.376, C.383, S.384, A.386 Ligands: OLA.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.365, A:L.368, A:P.369, A:I.373, A:F.376 Hydrogen bonds: A:S.384 Water bridges: A:S.384 CLR.5: 4 residues within 4Å: Chain A: C.375, F.376, F.379, C.380 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

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

OLC.6: 6 residues within 4Å: Chain A: T.90, F.95, C.96 Ligands: CLR.3, OLC.11, OLC.14 No protein-ligand interaction detected (PLIP) OLC.7: 4 residues within 4Å: Chain A: H.100, G.101, M.165 Ligands: CLR.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.100 OLC.8: 7 residues within 4Å: Chain A: C.53, V.56, W.57, V.71, I.78 Ligands: OLC.9, OLA.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.71, A:I.78 OLC.9: 6 residues within 4Å: Chain A: Y.68, K.147, I.150, W.154 Ligands: OLC.8, OLA.24 No protein-ligand interaction detected (PLIP) OLC.10: 4 residues within 4Å: Chain A: A.159, M.165, L.166 Ligands: OLA.24 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.159, A:L.166 OLC.11: 7 residues within 4Å: Chain A: I.89, T.90, T.93, F.95 Ligands: OLC.6, OLC.14, OLA.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.89 OLC.12: 1 residues within 4Å: Ligands: OLC.14 No protein-ligand interaction detected (PLIP) OLC.13: 7 residues within 4Å: Chain A: G.30, S.31, Y.34, S.92, L.388, Y.392 Ligands: OLA.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.34 Water bridges: A:S.31, A:S.31, A:S.31, A:S.92, A:S.92 OLC.14: 3 residues within 4Å: Ligands: OLC.6, OLC.11, OLC.12 No protein-ligand interaction detected (PLIP) OLC.27: 1 residues within 4Å: Ligands: CLR.3 No protein-ligand interaction detected (PLIP)

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

OLA.15: 2 residues within 4Å: Chain A: W.389 Ligands: OLA.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.389, A:W.389 OLA.16: 3 residues within 4Å: Chain A: G.30 Ligands: OLC.13, OLA.15 No protein-ligand interaction detected (PLIP) OLA.17: 1 residues within 4Å: Ligands: CLR.4 No protein-ligand interaction detected (PLIP) OLA.18: 3 residues within 4Å: Chain A: I.35, L.39 Ligands: OLC.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.39 OLA.19: 3 residues within 4Å: Chain A: S.32, I.35, T.36 No protein-ligand interaction detected (PLIP) OLA.20: 7 residues within 4Å: Chain A: F.69, F.118, A.122, I.125, V.141, I.149, C.153 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.125, A:I.125, A:I.149 Hydrogen bonds: A:A.122 OLA.21: 3 residues within 4Å: Chain A: Y.204, F.208, F.379 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.204, A:F.208 Water bridges: A:Y.204 OLA.22: 1 residues within 4Å: Chain A: G.361 No protein-ligand interaction detected (PLIP) OLA.23: 5 residues within 4Å: Chain A: L.44, L.47, G.48, W.54, F.407 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.407 OLA.24: 4 residues within 4Å: Chain A: W.154, F.158 Ligands: OLC.9, OLC.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.154, A:F.158 OLA.25: 4 residues within 4Å: Chain A: V.50, C.53, W.57 Ligands: OLC.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.50, A:W.57, A:W.57 Hydrogen bonds: A:W.57

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.26: 5 residues within 4Å: Chain A: T.144, R.145, G.148, I.149, I.152 No protein-ligand interaction detected (PLIP)

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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