SAXSdb — 9pxu

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1. Structure Basics

entry_id	9pxu
deposition_date	2025-08-06
title	Inactive-state naloxone-mu opioid receptor nanobody6 complex
keywords	G protein coupled receptor, Mu Opioid receptor, Naloxone, 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	45.89 Å
rg_electron	47.82 Å
i0	150844000.00
molecular_weight	101620.0 kDa
excluded_volume	127570 Å³
envelope_volume	192540 Å³
shell_volume	38474 Å³
envelope_diameter	164.1 Å
shell_rg	42.99 Å
envelope_rg	47.62 Å
shape_rg	47.79 Å
total_rg	47.69 Å
total_atoms	7167
n_residues	958
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	167.6 Å
rg_real	46.80 Å
rg_real_error	2.71 Å
i0_real	1.5080e+08
i0_real_error	3.3740e+06
rg_reciprocal	45.90 Å
i0_reciprocal	150700000.0000
total_estimate	0.7213
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	34.5 Å
skewness	0.599
kurtosis	-0.496
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	6515000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.443; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.380; Smooth: 0.663

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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
formula_weight	69550.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R
atom_count	7167

MKTIIALSYIFCLVFADYKDHDGDYKDHDIDYKDDDDKLHHHHHHHHHHLEVLFQGPGSGSADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGTGSDSSAAPTNASNCTDALAYSSCSPAPSPGSWVNLSHLDGNLSDPCGPNRTDLGGRDSLCPPTGSPSMITAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGTILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIINVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRLLSGSREKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALVTIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSNIEQQNSTRIRQNTRDHPSTANTVDRTNHQLENLEAETAPLPAAALEVLFQGPGSWSHPQFEKGGGSGGGSGGSSAWSHPQFEKHHHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Nanobody6
formula_weight	14418.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

QRQLVESGGGLVQPGGSLRLSCAASGTIFRLYDMGWFRQAPGKEREGVASITSGGSTKYADSVKGRFTISRDNAKNTVYLQMNSLEPEDTAVYYCNAEYRTGIWEELLDGWGKGTPVTVSSHHHHHHEPEA

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 3 polymer

description	Anti-fab nanobody
formula_weight	13764.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

MGSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSSLE

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 4 polymer

description	Nab-fab light chain
formula_weight	23258.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 5 polymer

description	Nab-fab heavy chain
formula_weight	25684.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSYYSIHWVRQAPGKGLEWVAYISSSSSYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGYQYWQYHASWYWNGGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 6 non-polymer

description	Naloxone
formula_weight	327.4 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	SODIUM ION
formula_weight	23.0 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	3.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.40 Å
resolution_method	—
num_particles	180003

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

Inactive-state naloxone-mu opioid receptor nanobody6 complex

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 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)