9YDR: PDB entry 9YDR

Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric modulator MIPS3983. Determined by electron microscopy at 2.14 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 2.14 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 8,254
Mol. weight: 134.71 kDa
Ligands: A1CU8
Released: 10 Dec 2025

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

Secondary structure: helices and β-sheets

9YDR contains 40 α-helices and 50 β-strands across 5 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-26	25
β-strand	28-35	8	1
α-helix	37-39	3
α-helix	41-43	3
β-strand	64-71	8	1
β-strand	74-81	8	1
α-helix	91-95	5
β-strand	100-106	7	1
α-helix	110-112	3
α-helix	113-125	13
β-strand	133-139	7	1
α-helix	141-150	10
α-helix	155-157	3
α-helix	160-162	3
α-helix	173-174	2
α-helix	179-198	20
β-strand	201	1	2
β-strand	204	1	2
β-strand	206-210	5	1
α-helix	218-238	21

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	135-140	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	175-181	7	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	218-223	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
α-helix	272	1
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	303-308	6	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	27-29	3
α-helix	30-43	14
α-helix	53-55	3

Chain N: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-98	7	12
β-strand	118	1	12
β-strand	122-124	3	12
β-strand	125-126	2	11

Chain R: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	43-73	31
α-helix	74-78	5
α-helix	83-98	16
α-helix	99-101	3
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	13
β-strand	195-200	6	13
α-helix	202-203	2
α-helix	206-218	13
α-helix	219-223	5
α-helix	224-240	17
α-helix	249-286	38
α-helix	294-315	22
α-helix	316-320	5
α-helix	323-332	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas	A	protein	245	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	350	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Nanobody 35	N	protein	156	Lama glama
Dadle	P	protein	5	Homo sapiens
OPRD1 isoform 1	R	protein	387	Homo sapiens	A0A6D2YBI2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9YDR_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas (chains A)
GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGADNSGKSTIVKQMRILHGGSG
GSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEA
LNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPG
EDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDVTDIIIKMNLR
DCGLF

Sequence of entity 2 (B), FASTA

>9YDR_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>9YDR_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (N), FASTA

>9YDR_4 Nanobody 35 (chains N)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVR
QAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR
CPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHH

Sequence of entity 5 (P), FASTA

>9YDR_5 DADLE (chains P)
YAGFL

Sequence of entity 6 (R), FASTA

>9YDR_6 OPRD1 isoform 1 (chains R)
DYKDDDDAEPAPSAGAELQPPLFANASDAYPSAFPSAGANASGPPGARSASSLALAIAIT
ALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFNLALADALATSTLPFQSAKYLMET
WPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPAKAKLINICIW
VLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKICVFLFAFVVPILIITVCY
GLMLLRLRSVRLLSGSKEKDRSLRRITRMVLVVVGAFVVCWAPIHIFVIVWTLVDIDRRD
PLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFRQLCRKPCGRPDPSSFSRAREATA
RERVTACTPSDGPGGGAAAHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1CU8	ethyl 3-[(8aS,9S,10S)-9-{4-[(2-cyclopropylphenyl)methoxy]phenyl}-6,6-dimethyl-8…	C31 H35 N5 O4	1

Primary citation

Structure-guided allosteric modulation of the delta opioid receptor. Mobbs, J.I., Nguyen, M.D., Deo, O. et al. bioRxiv (2025). DOI 10.1101/2025.10.16.682975 · PubMed

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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