SAXSdb — 9yfu

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1. Structure Basics

entry_id	9yfu
deposition_date	2025-09-26
title	Structure of GPR61 bound to inverse agonist compound 15
keywords	GPCR, GPR61, orphan receptor, inverse agonist, SIGNALING PROTEIN; SIGNALING 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	39.04 Å
rg_electron	39.16 Å
i0	277497000.00
molecular_weight	90821.0 kDa
excluded_volume	88299 Å³
envelope_volume	180810 Å³
shell_volume	39831 Å³
envelope_diameter	131.4 Å
shell_rg	43.12 Å
envelope_rg	38.30 Å
shape_rg	39.15 Å
total_rg	39.37 Å
total_atoms	6882
n_residues	891
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	129.0 Å
rg_real	39.16 Å
rg_real_error	1.35 Å
i0_real	2.7750e+08
i0_real_error	5.0340e+06
rg_reciprocal	39.09 Å
i0_reciprocal	277500000.0000
total_estimate	0.6016
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	48.4 Å
skewness	0.281
kurtosis	-0.591
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	12120000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.896; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	G-protein coupled receptor 61,Soluble cytochrome b562
formula_weight	59860.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R
atom_count	6883

YPYDVPDYAESSPIPQSSGNSSTLGRVPQTPGPSTASGVPEVGLRDVASESVALFFMLLLDLTAVAGNAAVMAVIAKTPALRKFVFVFHLCLVDLLAALTLMPLAMLSSSALFDHALFGEVACRLYLFLSVCFVSLAILSVSAINVERYYYVVHPMRYEVRMTLGLVASVLVGVWVKALAMASVPVLGRVSWEEGAPSVPPGCSLQWSHSAYCQLFVVVFAVLYFLLPLLLILVVYCSMFRARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLQKEVKAAVVLLAVGGQFLLCWLPYFSFHLYVALSAQPISTGQVESVVTWIGYFCFTSNPFFYGCLNRQIRGELSKQFVCFFKPAPEEELRLPSREGSIEENFLQFLQGTGCPSESWVSRPLPSPKQEPPAVDFRIPGQIAEETSEFLEQQLTSDIIMSDSYLRPAASPRLESGSDYKDDDDAK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Fab24 BAK5 heavy chain
formula_weight	24021.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EVQLVESGGGLVQPGGSLRLSCAASGFNVRSFSIHWVRQAPGKGLEWVAYISSSSGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Hinge-binding nanobody
formula_weight	14957.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

HHHHHHGENLYFQGSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYADSVQGRFTVSRDDAKTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	Fab24 BAK5 light chain
formula_weight	28884.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MKKNIAFLLASMFVFSIATNAYASDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEMKKNIAFLLASMFVFSIATNAYAEIS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 non-polymer

description	N-(5-chloro-4,6-dimethylpyrimidin-2-yl)-6-{[(3,5-difluoropyridin-4-yl)methyl]amino}-2-methylpyridine-3-sulfonamide
formula_weight	454.9 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
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	3.080 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.08 Å
resolution_method	—
num_particles	266475

fit	/app/data/saxs_computation/yf/9yfu/9yfu.fit
pddf	/app/data/pr_computation/yf/9yfu/9yfu.pr.out
profile	/app/data/saxs_computation/yf/9yfu/9yfu.dat

Structure of GPR61 bound to inverse agonist compound 15

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 (6)

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 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)