SAXSdb — 9ydr

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1. Structure Basics

entry_id	9ydr
deposition_date	2025-09-23
last_revision	2025-12-10
title	Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric modulator MIPS3983
keywords	GPCR, opioid receptor, ligand binding, allosteric modulation, 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	34.14 Å
rg_electron	34.16 Å
i0	404415000.00
molecular_weight	108030.0 kDa
excluded_volume	104190 Å³
envelope_volume	178080 Å³
shell_volume	44330 Å³
envelope_diameter	121.7 Å
shell_rg	39.73 Å
envelope_rg	34.47 Å
shape_rg	34.18 Å
total_rg	34.40 Å
total_atoms	8161
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	115.7 Å
rg_real	34.26 Å
rg_real_error	0.93 Å
i0_real	4.0440e+08
i0_real_error	6.7480e+06
rg_reciprocal	34.19 Å
i0_reciprocal	404400000.0000
total_estimate	0.8614
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	37.7 Å
skewness	0.490
kurtosis	-0.179
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	48960000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.747

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	8254

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	DADLE
formula_weight	569.6 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

YAGFL

Entity 6 polymer

description	OPRD1 isoform 1
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 7 non-polymer

description	;ethyl 3-[(8aS,9S,10S)-9-{4-[(2-cyclopropylphenyl)methoxy]phenyl}-6,6-dimethyl-8-oxo-7,8,8a,9-tetrahydrotetrazolo[5,1-b]quinazolin-4(6H)-yl]propanoate ;
formula_weight	541.6 kDa
src_method	syn
entity_count	1

Entity 8 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	2.140 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.14 Å
resolution_method	—
num_particles	319776

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

Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric modulator MIPS3983

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Source

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)