SMTL ID : 8jwy.1

Crystal structure of A2AR-T4L in complex with 2-118

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

monomer

Ligands

1 x VBF: 3-[2-azanyl-6-[2-oxidanylidene-1-[[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]methyl]pyridin-4-yl]pyrimidin-4-yl]-2-methyl-benzenecarbonitrile(Non-covalent)

VBF.1: 17 residues within 4Å: Chain A: Y.17, A.71, I.74, S.75, V.92, L.93, T.96, F.176, E.177, M.185, W.401, L.404, H.405, N.408, M.425, Y.426, I.429 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.17, A:V.92, A:F.176, A:F.176, A:F.176, A:W.401, A:L.404, A:L.404, A:M.425, A:Y.426, A:Y.426, A:I.429, A:I.429 Hydrogen bonds: A:N.408, A:N.408 Water bridges: A:N.189 Salt bridges: A:E.177 pi-Stacking: A:F.176, A:H.405

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 4 residues within 4Å: Chain A: F.190, C.409, F.410, C.414 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.190, A:F.410, A:F.410, A:F.410

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

OLA.3: 5 residues within 4Å: Chain A: P.403, I.406, I.407, F.410, L.424 Ligand excluded by PLIP OLA.4: 8 residues within 4Å: Chain A: Y.51, V.54, S.55, K.130, W.137 Ligands: OLA.5, OLA.13, OLA.21 Ligand excluded by PLIP OLA.5: 6 residues within 4Å: Chain A: C.36, W.40, A.58, A.62 Ligands: OLA.4, OLA.12 Ligand excluded by PLIP OLA.6: 11 residues within 4Å: Chain A: V.65, P.69, F.70, T.73, F.78, A.80, A.81, I.88, Q.171 Ligands: OLA.16, OLA.22 Ligand excluded by PLIP OLA.7: 8 residues within 4Å: Chain A: F.101, W.151, N.183, F.188, A.192, C.193 Ligands: OLA.9, OLA.17 Ligand excluded by PLIP OLA.8: 4 residues within 4Å: Chain A: L.200, G.203, V.204, R.207 Ligand excluded by PLIP OLA.9: 4 residues within 4Å: Chain A: N.183, Y.187, A.192 Ligands: OLA.7 Ligand excluded by PLIP OLA.10: 10 residues within 4Å: Chain A: L.27, L.30, G.31, L.34, P.440, F.441, A.444, F.454, R.455, I.458 Ligand excluded by PLIP OLA.12: 6 residues within 4Å: Chain A: V.33, C.36, W.37, W.40, V.65 Ligands: OLA.5 Ligand excluded by PLIP OLA.13: 2 residues within 4Å: Ligands: OLA.4, OLA.21 Ligand excluded by PLIP OLA.14: 7 residues within 4Å: Chain A: I.18, L.22, I.29, G.64, I.72, S.75, T.76 Ligand excluded by PLIP OLA.15: 4 residues within 4Å: Chain A: I.18, T.19, L.22, A.23 Ligand excluded by PLIP OLA.16: 6 residues within 4Å: Chain A: V.65, L.66, F.70, I.88 Ligands: OLA.6, OLA.22 Ligand excluded by PLIP OLA.17: 7 residues within 4Å: Chain A: L.139, A.142, I.143, T.146, W.151, F.188 Ligands: OLA.7 Ligand excluded by PLIP OLA.18: 7 residues within 4Å: Chain A: L.198, L.199, L.202, K.388, A.391, I.392, V.394 Ligand excluded by PLIP OLA.20: 11 residues within 4Å: Chain A: F.52, A.105, I.108, D.109, L.123, V.124, R.128, I.132, I.135, C.136, L.139 Ligand excluded by PLIP OLA.21: 8 residues within 4Å: Chain A: I.133, A.134, W.137, F.141, L.145 Ligands: OLA.4, OLA.13, OLA.22 Ligand excluded by PLIP OLA.22: 7 residues within 4Å: Chain A: A.81, H.83, G.84, F.87 Ligands: OLA.6, OLA.16, OLA.21 Ligand excluded by PLIP

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

NA.11: 4 residues within 4Å: Chain A: L.56, D.60, S.99, N.435 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.99, A:S.99, A:N.435 Water bridges: A:D.60

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

OLC.19: 7 residues within 4Å: Chain A: G.13, S.14, Y.17, Y.426, V.430, L.431, T.434 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.17, A:Y.426, A:Y.426, A:V.430, A:T.434

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weng, Y. et al., Structural insight into the dual-antagonistic mechanism of AB928 on adenosine A 2 receptors. Sci China Life Sci (2024)

Release Date

2023-08-16

Peptides

Adenosine receptor A2a,Endolysin: 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,Endolysin

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