SMTL ID : 6pt2.1

Crystal structure of the active delta opioid receptor in complex with the peptide agonist KGCHM07

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x DI7- DAR- PHE- SAR- OXJ: Peptide agonist KGCHM07(Non-covalent)

DI7-DAR-PHE-SAR-OXJ.1: 21 residues within 4Å: Chain A: Q.221, D.224, W.230, L.241, D.244, Y.245, M.248, C.314, V.333, W.390, I.393, H.394, F.396, V.397, W.400, I.405, R.407, V.412, L.416, I.420, Y.424 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Q.221, A:D.224, A:W.230, A:L.241, A:Y.245, A:Y.245, A:V.333, A:W.390, A:I.393, A:V.397, A:L.416, A:L.416 Hydrogen bonds: A:D.244 Water bridges: A:Y.245, A:Y.245, A:K.330, A:F.334 pi-Stacking: A:W.400, A:W.400 DI7-DAR-PHE-SAR-OXJ.2: 19 residues within 4Å: Chain B: Q.221, D.224, W.230, L.241, D.244, Y.245, M.248, C.314, V.333, W.390, I.393, H.394, F.396, V.397, W.400, I.405, R.407, L.416, Y.424 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Q.221, B:D.224, B:W.230, B:L.241, B:V.333, B:W.390, B:I.393, B:V.397, B:W.400, B:L.416, B:L.416 Hydrogen bonds: B:Y.245, B:Y.424 pi-Stacking: B:W.400, B:W.400

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 6 residues within 4Å: Chain A: A.391, P.392, I.395, V.399, I.405, V.412 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.391, A:P.392, A:P.392, A:I.395, A:I.395, A:V.399, A:I.405, A:V.412

7 x OLA: OLEIC ACID(Non-covalent)

OLA.4: 8 residues within 4Å: Chain A: S.173, S.222, A.223, L.226, M.227 Chain B: L.185, F.441, C.444 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.223, B:L.185, B:F.441 OLA.5: 9 residues within 4Å: Chain A: M.196, I.202, L.209, L.213, I.243, Y.246, K.282, N.285, W.289 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.202, A:L.209, A:L.213, A:I.243, A:Y.246, A:K.282, A:N.285, A:W.289, A:W.289, A:W.289 Salt bridges: A:K.282 OLA.6: 2 residues within 4Å: Chain B: Y.434, D.438 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.434, B:Y.434, B:Y.434 OLA.7: 1 residues within 4Å: Chain B: C.389 No protein-ligand interaction detected (PLIP) OLA.8: 4 residues within 4Å: Chain B: M.196, I.202, K.282, W.289 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.202, B:K.282, B:W.289, B:W.289 OLA.9: 2 residues within 4Å: Chain B: T.401, L.402 No protein-ligand interaction detected (PLIP) OLA.10: 3 residues within 4Å: Chain B: K.238, M.300, V.301 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.300 Salt bridges: B:K.238

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

OLC.11: 4 residues within 4Å: Chain B: P.392, V.399, I.405, V.412 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Claff, T. et al., Elucidating the active delta-opioid receptor crystal structure with peptide and small-molecule agonists. Sci Adv (2019)

Release Date

2019-12-11

Peptides

Delta opioid receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Delta opioid receptor

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