9XF4: Leu-enkephalin-BMS-986187-bound DOR-Gi2 complex

Cryo-EM structure of Leu-enkephalin-BMS-986187-bound DOR-Gi2 complex. Determined by electron microscopy at 3.05 Å resolution. Released 8 Jul 2026.

Method: Electron microscopy
Resolution: 3.05 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 5
Atoms: 7,142
Mol. weight: 157.45 kDa
Ligands: A1D6B
Released: 8 Jul 2026

Explore 9XF4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XF4 contains 26 α-helices and 40 β-strands across 4 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: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	48-76	29
α-helix	83-99	17
α-helix	102-110	9
α-helix	118-151	34
α-helix	153-159	7
α-helix	162-186	25
β-strand	187-192	6	1
β-strand	195-200	6	1
α-helix	209-218	10
α-helix	219-223	5
α-helix	224-239	16
α-helix	250-286	37
α-helix	294-318	25
α-helix	323-329	7

Chain B: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	17-24	8
α-helix	30-34	5
α-helix	38-40	3
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	91-94	4	3
β-strand	102-105	4	4
β-strand	111-115	5	4
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	148-151	4	5
β-strand	157-161	5	5
β-strand	166-170	5	5
β-strand	175-180	6	5
β-strand	187	1	6
β-strand	191-192	2	7
β-strand	198-202	5	7
β-strand	203	1	6
β-strand	208-212	5	7
β-strand	217-222	6	7
β-strand	232-234	3	8
β-strand	240-243	4	8
β-strand	249-254	6	8
β-strand	259-265	7	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	293-298	6	9
β-strand	304-309	6	9
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-23	15
α-helix	30-43	14

Chain D: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-30	25
α-helix	33	1
β-strand	34-37	4	10
α-helix	46-54	9
β-strand	186-192	7	10
β-strand	195-201	7	10
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	10
β-strand	234	1	11
β-strand	242	1	11
α-helix	243-255	13
β-strand	264-270	7	10
α-helix	274-277	4
α-helix	297-309	13
β-strand	320-324	5	10
α-helix	333-351	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Delta-type opioid receptor,Oplophorus-luciferin 2-monooxygenase catalytic…	A	protein	595	Escherichia coli, Homo sapiens, synthetic construct	P41143 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	384	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-2	D	protein	355	Homo sapiens	P04899 (AlphaFold model)
Tyr-gly-gly-phe-leu	L	protein	5	synthetic construct

Sequence of entity 1 (A), FASTA

>9XF4_1 Soluble cytochrome b562,Delta-type opioid receptor,Oplophorus-luciferin 2-monooxygenase catalytic subunit (chains A)
MKTIIALSYIFCLVFADYKDDDDAADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAA
ALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKT
TRNAYIQKYLRSASSLALAIAITALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFN
LALADALATSTLPFQSAKYLMETWPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAV
CHPVKALDFRTPAKAKLINICIAVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWD
TVTKICVFLFAFVVPILIITVCYGLMLLRLRSVRLLSGSKEKDRSLRRITRMVLVVVGAF
VVCWAPIHIFVIVWTLVDIDRRDPLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFR
QLCRKPCGRPDPSSFSRVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQ
RIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGV
TPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Sequence of entity 2 (B), FASTA

>9XF4_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGG
SGGGGSGGSSSGGVSGWRLFKKIS

Sequence of entity 3 (C), FASTA

>9XF4_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (D), FASTA

>9XF4_4 Guanine nucleotide-binding protein G(i) subunit alpha-2 (chains D)
MGCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEDG
YSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVL
PDDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVLRTRV
KTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEE
MNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGANKYDEA
ASYIQSKFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 5 (L), FASTA

>9XF4_5 TYR-GLY-GLY-PHE-LEU (chains L)
YGGFL

Ligands and cofactors

ID	Name	Formula	Copies
A1D6B	3,3,6,6-tetramethyl-9-[4-[(2-methylphenyl)methoxy]phenyl]-4,5,7,9-tetrahydro-2~…	C31 H34 O4	1

Primary citation

Molecular mechanism of allosteric modulation of opioid receptors. Wang, H., Miao, Z., Zhao, C. et al. Signal Transduct Target Ther (2026) 11. DOI 10.1038/s41392-026-02759-5 · 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
6PT2 2.8 Å, Crystal structure of the active delta opioid receptor in complex with the peptide…
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
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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