SMTL ID : 4n6h.1

1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

12 x OLA: OLEIC ACID(Non-covalent)

OLA.1: 4 residues within 4Å: Chain A: P.179, P.191, F.192 Ligands: OLA.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.179, A:F.192, A:F.192 OLA.2: 6 residues within 4Å: Chain A: M.147, F.148, V.151, A.172, S.176 Ligands: OLC.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.148, A:A.172 OLA.3: 4 residues within 4Å: Chain A: V.363, D.364, I.365 Ligands: OLA.4 No protein-ligand interaction detected (PLIP) OLA.4: 9 residues within 4Å: Chain A: P.352, I.355, F.356, I.365, D.366, V.372 Ligands: OLA.3, OLA.10, OLA.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.355, A:F.356, A:I.365, A:V.372 Hydrogen bonds: A:D.366 OLA.5: 8 residues within 4Å: Chain A: Y.309, L.313, R.337, G.344, A.345, V.348, L.382 Ligands: OLA.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.348, A:L.382 OLA.6: 10 residues within 4Å: Chain A: Y.163, M.217, D.221, I.224, F.235, R.236, T.237, K.240, A.241, I.244 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.224, A:F.235, A:I.244 Hydrogen bonds: A:D.221, A:T.237 Water bridges: A:Y.163, A:D.221 OLA.9: 4 residues within 4Å: Chain A: A.127, A.130, L.131, A.134 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.127, A:A.130, A:L.131, A:A.134 OLA.10: 4 residues within 4Å: Chain A: D.369, L.371, V.372 Ligands: OLA.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.371 OLA.11: 3 residues within 4Å: Chain A: A.123, L.124, A.127 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.127 OLA.15: 5 residues within 4Å: Chain A: Y.309, L.313, V.348 Ligands: OLA.4, OLA.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.313, A:V.348 OLA.16: 5 residues within 4Å: Chain A: R.337, L.389, V.392, F.396, L.397 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.389, A:V.392, A:F.396, A:F.396, A:L.397 Salt bridges: A:R.337 OLA.17: 3 residues within 4Å: Chain A: P.191, F.192 Ligands: OLA.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.192 Hydrogen bonds: A:P.191

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

OLC.7: 7 residues within 4Å: Chain A: F.213, M.217, C.247, I.248, L.251, V.300 Ligands: PGE.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.251, A:V.300 OLC.8: 5 residues within 4Å: Chain A: S.253, P.258, V.261, M.262, Q.277 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.258 Hydrogen bonds: A:Q.277 OLC.12: 4 residues within 4Å: Chain A: F.165, K.242 Ligands: OLA.2, OLC.22 No protein-ligand interaction detected (PLIP) OLC.22: 13 residues within 4Å: Chain A: I.150, K.157, I.162, F.165, N.166, L.169, K.242, N.245, W.249, V.250, S.253 Ligands: OLC.12, OLC.23 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.165, A:N.245, A:W.249, A:V.250 Hydrogen bonds: A:N.245 OLC.23: 9 residues within 4Å: Chain A: L.195, K.198, A.199, I.203, Y.206, W.249, M.260, V.261 Ligands: OLC.22 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.198, A:A.199, A:I.203, A:Y.206, A:W.249 Hydrogen bonds: A:K.198 Salt bridges: A:K.198

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.13: 3 residues within 4Å: Chain A: I.291, L.295, I.358 No protein-ligand interaction detected (PLIP) PGE.14: 2 residues within 4Å: Chain A: M.217 Ligands: OLC.7 No protein-ligand interaction detected (PLIP) PGE.21: 3 residues within 4Å: Chain A: T.287, V.288, I.291 No protein-ligand interaction detected (PLIP)

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.18: 7 residues within 4Å: Chain A: T.158, A.159, T.160, R.222, R.236, L.332, I.335 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.159, A:T.160, A:T.160, A:R.222, A:R.222, A:R.236, A:R.236 Salt bridges: A:R.222, A:R.236

1 x EJ4: (4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol(Non-covalent)

EJ4.19: 13 residues within 4Å: Chain A: D.204, Y.205, M.208, K.290, V.293, W.350, I.353, H.354, V.357, W.360, I.380, G.383, Y.384 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.205, A:V.293, A:W.350, A:I.353, A:V.357, A:V.357, A:Y.384 Water bridges: A:Y.205, A:Y.205, A:Y.205, A:Y.205 Salt bridges: A:D.204

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

NA.20: 3 residues within 4Å: Chain A: D.171, N.207, S.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.171, A:N.207, A:S.211 Water bridges: A:S.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenalti, G. et al., Molecular control of delta-opioid receptor signalling. Nature (2014)

Release Date

2013-12-25

Peptides

Soluble cytochrome b562, Delta-type opioid receptor chimeric protein: 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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Soluble cytochrome b562, Delta-type opioid receptor chimeric protein