6PT2: Active delta opioid receptor

Crystal structure of the active delta opioid receptor in complex with the peptide agonist KGCHM07. Determined by X-ray diffraction at 2.8 Å resolution. Released 11 Dec 2019.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 5,972
Mol. weight: 106.49 kDa
Ligands: OLC, OLA, CLR
Released: 11 Dec 2019

Explore 6PT2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PT2 contains 42 α-helices and 6 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1000-1018	19
α-helix	1023-1040	18
α-helix	1056-1081	26
α-helix	1086-1089	4
α-helix	1092-1097	6
α-helix	1098-1102	5
α-helix	1103-1105	3
β-strand	42-44	3	1
α-helix	46-76	31
α-helix	83-99	17
α-helix	102-111	10
α-helix	118-151	34
α-helix	156-159	4
α-helix	162-175	14
α-helix	177-186	10
β-strand	187-192	6	2
β-strand	195-200	6	2
α-helix	202	1
α-helix	206-218	13
α-helix	219-223	5
α-helix	224-246	23
α-helix	254-286	33
α-helix	294-321	28
α-helix	323-328	6

Chain B: 21 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1003-1017	15
α-helix	1024-1041	18
α-helix	1059-1077	19
α-helix	1093-1097	5
α-helix	1098-1100	3
α-helix	42-73	32
α-helix	74-78	5
α-helix	83-99	17
α-helix	102-111	10
α-helix	117-151	35
α-helix	153-159	7
α-helix	162-175	14
α-helix	177-186	10
β-strand	187-192	6	3
β-strand	195-200	6	3
α-helix	202-203	2
α-helix	206-218	13
α-helix	219-223	5
α-helix	224-241	18
α-helix	251-286	36
α-helix	294-312	19
α-helix	315-324	10
α-helix	326-329	4
β-strand	330-332	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Delta opioid receptor	A, B	protein	454	Homo sapiens	P41143 (AlphaFold model)
Peptide agonist KGCHM07	C, D	protein	5	synthetic construct

Sequence of entity 1 (A, B), FASTA

>6PT2_1 Delta opioid receptor (chains A, B)
MKTIIALSYIFCLVFADYKDDDDAKLQTMHHHHHHHHHHENLYFQGGTTMADLEDNWETL
NDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVG
QIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLRSASSLALAIAITALYSAVCAVGL
LGNVLVMFVIVRYTKMKTATNIYIFSLALAGALATSTLPFQSADYLMETWPFGELLCKAV
LSIDYYSMFTSIFTLTMMCVDRYIAVCHPVKALDFRTPAKAKLINICIWVLASGVGVPIM
VMAVTRPRDGAVVCMLQFPSPSWYWDTVTKICVFLFAFVVPILIITVCYGLMLLRLRSVR
LLSGSKEKDRSLRRITRMVLVVVVAFVVCWAPIHIFVIVWTLVDIDRRDPLVVAALHLCI
ALGYINSSLNPVLYAFLDKNFKRCFRQLCRKPCG

Sequence of entity 2 (C, D), FASTA

>6PT2_2 Peptide agonist KGCHM07 (chains C, D)
YRFGX

Ligands and cofactors

ID	Name	Formula	Copies
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	1
OLA	Oleic acid	C18 H34 O2	7
CLR	Cholesterol	C27 H46 O	1

Primary citation

Elucidating the active delta-opioid receptor crystal structure with peptide and small-molecule agonists. Claff, T., Yu, J., Blais, V. et al. Sci Adv (2019) 5:eaax9115-eaax9115. DOI 10.1126/sciadv.aax9115 · PubMed

Other PDB entries of the same protein (UniProt P41143 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4N6H 1.8 Å, 1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
9CGK 2.62 Å, CryoEM structure of delta opioid receptor bound to G proteins and a full bitopic agonist
4RWD 2.7 Å, XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide
9XDQ 2.79 Å, Cryo-EM structure of BMS986187 bound DOR-Gi complex
9CGJ 2.8 Å, CryoEM structure of delta opioid receptor bound to G proteins and a partial agonist
8Y71 2.97 Å, positive allosteric modulator(BMS986187)-bound delta-opioid receptor-Gi complex
8F7S 3.0 Å, Gi bound delta-opioid receptor in complex with deltorphin
9PPX 3.04 Å, CryoEM structure of delta opioid receptor bound to G proteins and naltrexone
9XF4 3.05 Å, Cryo-EM structure of Leu-enkephalin-BMS-986187-bound DOR-Gi2 complex
9PPY 3.1 Å, CryoEM structure of delta opioid receptor bound to G proteins and met-enkephalin
9PQ0 3.12 Å, CryoEM structure of delta opioid receptor bound to G proteins and ADL5859

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