SMTL ID : 5jtb.1

Crystal structure of the chimeric protein of A2aAR-BRIL with bound iodide ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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: 13 residues within 4Å: Chain A: L.110, F.193, E.194, M.199, M.202, W.367, L.370, H.371, N.374, H.385, L.388, M.391, I.395 10 PLIP interactions: 10 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:F.193 Salt bridges: A:E.194 pi-Stacking: A:F.193, A:F.193

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 7 residues within 4Å: Chain A: F.87, A.97, A.98, G.101, F.104, I.105 Ligands: OLC.20 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.87, A:A.97, A:A.98, A:F.104, A:I.105, A:I.105 Hydrogen bonds: A:A.98, A:Q.188 CLR.3: 9 residues within 4Å: Chain A: P.369, I.372, I.373, F.376, C.383, S.384, A.386, L.390 Ligands: OLA.13 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.369, A:I.372, A:I.372, A:I.373, A:F.376, A:L.390 Hydrogen bonds: A:S.384 CLR.4: 8 residues within 4Å: Chain A: F.207, F.208, L.212, C.375, F.376, F.379, C.380 Ligands: OLC.18 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.207, A:F.208, A:L.212, A:F.376, A:F.376, A:F.376, A:F.379, A:F.379

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: K.422 Ligand excluded by PLIP IOD.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: R.132, A.228, R.231, Q.232 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: I.133, P.134, L.135 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: Q.347, V.350 Ligand excluded by PLIP

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

PEG.11: 4 residues within 4Å: Chain A: T.144, R.145, G.148 Ligands: PEG.12 No protein-ligand interaction detected (PLIP) PEG.12: 2 residues within 4Å: Chain A: R.145 Ligands: PEG.11 No protein-ligand interaction detected (PLIP)

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

OLA.13: 6 residues within 4Å: Chain A: S.384, H.385, W.389, L.390, L.393 Ligands: CLR.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.389, A:W.389, A:L.390, A:L.393 Hydrogen bonds: A:S.384 OLA.14: 7 residues within 4Å: Chain A: P.86, I.89, T.90, T.93, F.95 Ligands: OLA.16, OLC.20 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.89 OLA.15: 8 residues within 4Å: Chain A: G.30, S.31, Y.34, V.37, L.388, W.389, Y.392, V.396 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.34, A:V.37, A:L.388 OLA.16: 2 residues within 4Å: Ligands: OLA.14, OLC.20 No protein-ligand interaction detected (PLIP)

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

OLC.17: 6 residues within 4Å: Chain A: Y.68, V.71, A.75, I.150, W.154 Ligands: OLB.23 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.75, A:W.154, A:W.154 OLC.18: 5 residues within 4Å: Chain A: F.208, L.212, F.379 Ligands: CLR.4, OLC.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.208, A:L.212, A:F.379 OLC.19: 3 residues within 4Å: Chain A: H.100, M.165, L.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.100 OLC.20: 6 residues within 4Å: Chain A: T.90, F.95, C.96 Ligands: CLR.2, OLA.14, OLA.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.95 OLC.21: 1 residues within 4Å: Chain A: M.165 No protein-ligand interaction detected (PLIP) OLC.22: 5 residues within 4Å: Chain A: Y.204, F.208, V.213, F.379 Ligands: OLC.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.208, A:V.213

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

OLB.23: 10 residues within 4Å: Chain A: C.53, V.56, W.57, Q.63, Y.68, V.71, A.75, I.78, A.79 Ligands: OLC.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.71, A:A.75, A:A.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Melnikov, I. et al., Fast iodide-SAD phasing for high-throughput membrane protein structure determination. Sci Adv (2017)

Release Date

2017-05-31

Peptides

Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a: 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,Adenosine receptor A2a

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