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9s1x

Crystal structure of human IDO1 in complex with iDeg-9

Method: X-RAY DIFFRACTION D_max: 73.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s1x
deposition_date	2025-07-21
title	Crystal structure of human IDO1 in complex with iDeg-9
keywords	IDO1, heme-binding protein, pseudo-natural product, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

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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	22.68 Å
rg_electron	21.43 Å
i0	30435800.00
molecular_weight	44030.0 kDa
excluded_volume	55827 Å³
envelope_volume	63954 Å³
shell_volume	24767 Å³
envelope_diameter	76.5 Å
shell_rg	28.45 Å
envelope_rg	21.64 Å
shape_rg	21.41 Å
total_rg	22.40 Å
total_atoms	6215
n_residues	382
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	73.7 Å
rg_real	22.63 Å
rg_real_error	0.41 Å
i0_real	3.0440e+07
i0_real_error	3.6070e+05
rg_reciprocal	22.64 Å
i0_reciprocal	30440000.0000
total_estimate	0.8859
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.8 Å
skewness	0.338
kurtosis	-0.204
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	8394000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Indoleamine 2,3-dioxygenase 1
formula_weight	45367.2 kDa
ec_number	1.13.11.52
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6385

GPLGSGIQMENSWTISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	;2-[4-[[(1~{R},2~{S},6~{S},8~{R})-2-[(4-ethynylphenyl)carbamoyloxymethyl]-9,9-dimethyl-4-azatricyclo[6.1.1.0^{2,6}]decan-4-yl]sulfonyl]-3-methyl-phenyl]-2-methyl-propanoic acid ;
formula_weight	578.7 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	113

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6. Citations (1)

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length_a	106.750 Å
length_b	109.650 Å
length_c	36.010 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.000 Å
resolution_low	48.770 Å
r_factor	0.1860
r_work	0.1834
r_free	0.2216

fit	/app/data/saxs_computation/s1/9s1x/9s1x.fit
pddf	/app/data/pr_computation/s1/9s1x/9s1x.pr.out
profile	/app/data/saxs_computation/s1/9s1x/9s1x.dat

Crystal structure of human IDO1 in complex with iDeg-9

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

Diffraction