SAXSdb — 9ydp

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1. Structure Basics

entry_id	9ydp
deposition_date	2025-09-23
last_revision	2025-12-10
title	Human delta opioid receptor complex with mini-Gi and agonist DADLE
keywords	GPCR, opioid receptor, ligand binding, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	34.07 Å
rg_electron	34.25 Å
i0	205991000.00
molecular_weight	115680.0 kDa
excluded_volume	144900 Å³
envelope_volume	178870 Å³
shell_volume	44478 Å³
envelope_diameter	121.3 Å
shell_rg	39.71 Å
envelope_rg	34.57 Å
shape_rg	34.24 Å
total_rg	34.66 Å
total_atoms	8121
n_residues	1048
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	115.8 Å
rg_real	34.21 Å
rg_real_error	0.82 Å
i0_real	2.0600e+08
i0_real_error	3.3370e+06
rg_reciprocal	34.12 Å
i0_reciprocal	206000000.0000
total_estimate	0.8560
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.8 Å
skewness	0.514
kurtosis	-0.120
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	47650000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.719

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
formula_weight	27915.7 kDa
ec_number	3.6.5.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8214

GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGADNSGKSTIVKQMRILHGGSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDVTDIIIKMNLRDCGLF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	38534.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
formula_weight	7861.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 4 polymer

description	nanobody 35
formula_weight	16926.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHH

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

Entity 5 polymer

description	Delta-type opioid receptor
formula_weight	42363.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

DYKDDDDAEPAPSAGAELQPPLFANASDAYPSAFPSAGANASGPPGARSASSLALAIAITALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFNLALADALATSTLPFQSAKYLMETWPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPAKAKLINICIWVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKICVFLFAFVVPILIITVCYGLMLLRLRSVRLLSGSKEKDRSLRRITRMVLVVVGAFVVCWAPIHIFVIVWTLVDIDRRDPLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFRQLCRKPCGRPDPSSFSRAREATARERVTACTPSDGPGGGAAAHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 6 polymer

description	DADLE
formula_weight	569.6 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

YAGFL

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	93

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.950 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	1.95 Å
resolution_method	—
num_particles	1245037

fit	/app/data/saxs_computation/yd/9ydp/9ydp.fit
pddf	/app/data/pr_computation/yd/9ydp/9ydp.pr.out
profile	/app/data/saxs_computation/yd/9ydp/9ydp.dat

Human delta opioid receptor complex with mini-Gi and agonist DADLE

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)