SMTL ID : 8f7s.1

Gi bound delta-opioid receptor in complex with deltorphin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

2 x TYR- DAL- PHE- GLU- VAL- VAL- GLY- NH2: deltorphin(Non-covalent)

TYR-DAL-PHE-GLU-VAL-VAL-GLY-NH2.1: 19 residues within 4Å: Chain A: Q.115, K.118, W.124, L.135, D.138, Y.139, M.142, V.207, C.208, L.210, K.224, V.227, I.287, V.291, W.294, R.301, L.310, I.314, Y.318 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.115, A:W.124, A:L.135, A:Y.139, A:I.287, A:V.291, A:L.310 Hydrogen bonds: A:D.138, A:Y.139, A:C.208, A:R.301, A:Y.318 Salt bridges: A:K.224 TYR-DAL-PHE-GLU-VAL-VAL-GLY-NH2.2: 20 residues within 4Å: Chain E: Q.115, K.118, W.124, L.135, D.138, Y.139, M.142, V.207, C.208, L.210, K.224, V.227, I.287, V.291, W.294, R.301, L.310, H.311, I.314, Y.318 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:Q.115, E:W.124, E:L.135, E:Y.139, E:V.291 Hydrogen bonds: E:D.138, E:C.208, E:R.301, E:Y.318 Salt bridges: E:K.224

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 4 residues within 4Å: Chain A: M.90, F.99, L.103 Ligands: CLR.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.99, A:L.103 CLR.4: 8 residues within 4Å: Chain A: M.81, F.82, V.85, R.86, L.103, L.107, S.110 Ligands: CLR.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.82, A:V.85, A:L.103, A:L.107 Hydrogen bonds: A:R.86 CLR.14: 5 residues within 4Å: Chain E: M.90, F.99, L.103, L.107 Ligands: CLR.15 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.99, E:L.103, E:L.107 CLR.15: 6 residues within 4Å: Chain E: M.81, F.82, V.85, R.86, S.110 Ligands: CLR.14 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.85 Hydrogen bonds: E:R.86 CLR.16: 7 residues within 4Å: Chain E: V.189, I.193, P.213, W.219, T.223, V.227 Ligands: PLM.11 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:V.189, E:I.193, E:P.213, E:W.219, E:W.219, E:T.223, E:V.227

12 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 3 residues within 4Å: Chain A: R.264, R.268, R.271 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.268 Salt bridges: A:R.271 PLM.6: 6 residues within 4Å: Chain A: A.285, P.286, F.290, V.293 Chain E: A.285, P.286 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:A.285, E:P.286, A:A.285, A:F.290 PLM.7: 3 residues within 4Å: Chain A: Y.157, H.162, V.241 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.162 PLM.8: 2 residues within 4Å: Chain A: A.71, L.120 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.71 PLM.9: 8 residues within 4Å: Chain A: Y.139, V.189, I.193, M.196, P.213, W.219, T.223, V.227 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.139, A:V.189, A:P.213, A:W.219, A:W.219, A:T.223, A:V.227 PLM.10: 3 residues within 4Å: Chain A: I.299 Chain E: A.279, L.316 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:A.279, E:L.316, A:I.299 PLM.11: 3 residues within 4Å: Chain A: R.251 Chain E: C.226 Ligands: CLR.16 No protein-ligand interaction detected (PLIP) PLM.12: 5 residues within 4Å: Chain A: A.279, V.282, L.316 Chain E: V.297, I.299 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:V.297, E:V.297, A:V.282, A:L.316 PLM.13: 3 residues within 4Å: Chain A: W.219, C.226 Chain E: R.251 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.219 PLM.17: 3 residues within 4Å: Chain E: R.268, R.271, L.327 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:R.268, E:L.327 Salt bridges: E:R.271 PLM.18: 5 residues within 4Å: Chain E: Y.157, H.162, L.237, I.238, V.241 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.237, E:I.238, E:V.241 Salt bridges: E:H.162 PLM.19: 3 residues within 4Å: Chain E: S.67, A.71, L.120 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structures of the entire human opioid receptor family. Cell (2023)

Release Date

2022-12-14

Peptides

Delta-type opioid receptor: AE
Guanine nucleotide-binding protein G(i) subunit alpha-1: BF
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: C
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

E
D

B
A

F
F

C
B

D
C

Membrane

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

Guanine nucleotide-binding protein G(i) subunit alpha-1

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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