SMTL ID : 4xnv.1

The human P2Y1 receptor in complex with BPTU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x BUR: 1-[2-(2-tert-butylphenoxy)pyridin-3-yl]-3-[4-(trifluoromethoxy)phenyl]urea(Non-covalent)

BUR.1: 12 residues within 4Å: Chain A: F.61, F.65, L.101, T.102, P.104, A.105, F.118, M.122, L.125, Q.126 Ligands: Y01.5, 1PE.14 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.65, A:L.101, A:T.102, A:P.104, A:A.105, A:L.125, A:Q.126 Hydrogen bonds: A:L.101, A:L.101 pi-Stacking: A:F.61, A:F.118

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 7 residues within 4Å: Chain A: V.180, P.184, Y.188, S.212, Y.216, C.219 Ligands: OLC.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.184, A:Y.216

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 12 residues within 4Å: Chain A: A.318, I.322, P.323, V.326, M.327, M.330, F.346, R.349, V.350, T.353 Ligands: OLC.6, OLC.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.322, A:I.322, A:P.323, A:V.326, A:F.346, A:V.350 Hydrogen bonds: A:R.349 Salt bridges: A:R.349 Y01.4: 12 residues within 4Å: Chain A: Y.88, L.139, T.142, C.143, A.146, H.147, S.150, I.170, I.177, A.223, V.227, L.231 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.139, A:T.142, A:A.146, A:I.170, A:I.170, A:V.227, A:L.231 Hydrogen bonds: A:Y.88, A:S.150 Salt bridges: A:H.147 Y01.5: 12 residues within 4Å: Chain A: I.58, F.61, I.62, F.65, L.66, P.104, I.107, F.108, F.111, N.112 Ligands: BUR.1, 1PE.14 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.58, A:F.61, A:F.61, A:I.62, A:F.65, A:L.66, A:I.107, A:F.108, A:F.108, A:F.111, A:F.111

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

OLC.6: 5 residues within 4Å: Chain A: V.326, M.330, F.346 Ligands: Y01.3, OLC.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.326 OLC.7: 9 residues within 4Å: Chain A: V.180, S.183, P.184, F.187, Y.188, Y.209, S.212 Ligands: CLR.2, OLC.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.180, A:V.180, A:P.184, A:P.184, A:F.187, A:F.187 Water bridges: A:E.208 OLC.8: 7 residues within 4Å: Chain A: D.120, A.121, K.124, L.125, F.128, L.186 Ligands: OLC.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.121, A:L.125, A:F.128, A:L.186 Hydrogen bonds: A:D.120 OLC.9: 9 residues within 4Å: Chain A: K.45, F.48, Y.52, L.59, I.63, V.356, L.363, C.366, I.370 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.52, A:I.63, A:V.356, A:L.363, A:L.363, A:I.370 Hydrogen bonds: A:K.45, A:F.48 OLC.10: 8 residues within 4Å: Chain A: D.120, K.124, V.179, S.183, L.186, F.187 Ligands: OLC.7, OLC.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.179, A:L.186, A:L.186 Hydrogen bonds: A:D.120 Salt bridges: A:K.124 OLC.11: 10 residues within 4Å: Chain A: F.50, Y.51, P.54, A.55, I.58, L.59, I.62, I.63, Y.110, F.111 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.55, A:I.58, A:I.58, A:L.59, A:I.62, A:I.63, A:F.111 OLC.12: 11 residues within 4Å: Chain A: T.221, F.225, C.226, L.229, V.230, H.325, V.326, T.329, M.330, R.333 Ligands: OLC.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.221, A:F.225, A:L.229, A:V.230, A:V.326 Hydrogen bonds: A:R.333 OLC.13: 11 residues within 4Å: Chain A: L.314, T.315, A.318, V.319, P.323, R.349, A.352, T.353, V.356, L.360 Ligands: Y01.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.314, A:A.318, A:P.323, A:T.353, A:V.356, A:L.360 Hydrogen bonds: A:T.353

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.14: 3 residues within 4Å: Chain A: P.104 Ligands: BUR.1, Y01.5 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.15: 4 residues within 4Å: Chain A: C.252, C.255, C.285, C.288 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.252, A:C.255, A:C.285, A:C.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, D. et al., Two disparate ligand-binding sites in the human P2Y1 receptor. Nature (2015)

Release Date

2015-04-01

Peptides

P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1: 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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P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1

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