SAXSdb — 9pxy

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1. Structure Basics

entry_id	9pxy
deposition_date	2025-08-06
title	Primed-state naloxone-mu opioid receptor-Gi GDPbS complex (rebound)
keywords	G protein coupled receptor, Mu Opioid receptor, Naloxone, MEMBRANE PROTEIN, GDP; 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	35.78 Å
rg_electron	36.08 Å
i0	204131000.00
molecular_weight	116390.0 kDa
excluded_volume	146310 Å³
envelope_volume	194750 Å³
shell_volume	46303 Å³
envelope_diameter	130.2 Å
shell_rg	40.73 Å
envelope_rg	36.35 Å
shape_rg	36.08 Å
total_rg	36.41 Å
total_atoms	8160
n_residues	1020
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	121.3 Å
rg_real	35.88 Å
rg_real_error	1.07 Å
i0_real	2.0410e+08
i0_real_error	3.8410e+06
rg_reciprocal	35.82 Å
i0_reciprocal	204100000.0000
total_estimate	0.8656
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.1 Å
skewness	0.431
kurtosis	-0.177
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	52170000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.752

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Soluble cytochrome b562,Mu-type opioid receptor,Soluble cytochrome b562,Mu-type opioid receptor,Mu opioid receptor
formula_weight	69540.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R
atom_count	8160

MKTIIALSYIFCLVFADYKDHDGDYKDHDIDYKDDDDKLHHHHHHHHHHLEVLFQGPGSGSADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGTGSDSSAAPTNASNCTDALAYSSCSPAPSPGSWVNLSHLDGNLSDPCGPNRTDLGGRDSLCPPTGSPSMITAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGTILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIINVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALVTIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSNIEQQNSTRIRQNTRDHPSTANTVDRTNHQLENLEAETAPLPAAALEVLFQGPGSWSHPQFEKGGGSGGGSGGSSAWSHPQFEKHHHHHHHHHH

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Guanine nucleotide-binding protein G(i) subunit alpha-1
formula_weight	40415.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	39839.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

HHHHHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 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	C

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	Naloxone
formula_weight	327.4 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine
formula_weight	459.3 kDa
src_method	syn
entity_count	1

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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	3.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.00 Å
resolution_method	—
num_particles	218106

fit	/app/data/saxs_computation/px/9pxy/9pxy.fit
pddf	/app/data/pr_computation/px/9pxy/9pxy.pr.out
profile	/app/data/saxs_computation/px/9pxy/9pxy.dat

Primed-state naloxone-mu opioid receptor-Gi GDPbS complex (rebound)

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 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)