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9ris

Crystal structure of human IDO1 in complex with iDeg-1

Method: X-RAY DIFFRACTION D_max: 75.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ris
deposition_date	2025-06-11
title	Crystal structure of human IDO1 in complex with iDeg-1
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	22.58 Å
rg_electron	21.34 Å
i0	28148100.00
molecular_weight	42216.0 kDa
excluded_volume	53530 Å³
envelope_volume	60917 Å³
shell_volume	23862 Å³
envelope_diameter	76.5 Å
shell_rg	28.18 Å
envelope_rg	21.60 Å
shape_rg	21.31 Å
total_rg	22.35 Å
total_atoms	5952
n_residues	365
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	75.7 Å
rg_real	22.55 Å
rg_real_error	0.41 Å
i0_real	2.8150e+07
i0_real_error	3.5120e+05
rg_reciprocal	22.56 Å
i0_reciprocal	28150000.0000
total_estimate	0.8751
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	26.4 Å
skewness	0.363
kurtosis	-0.194
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	7375000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.980

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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	6113

GPLGSGIQMENSWTISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	nat
entity_count	2

Entity 3 non-polymer

description	;[(1~{R},2~{S},6~{S},8~{R})-4-(4-~{tert}-butylphenyl)sulfonyl-9,9-dimethyl-4-azatricyclo[6.1.1.0^{2,6}]decan-2-yl]methyl ~{N}-(4-methylphenyl)carbamate ;
formula_weight	524.7 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	51

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6. Citations (1)

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length_a	105.270 Å
length_b	110.170 Å
length_c	36.140 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	2.100 Å
resolution_low	48.810 Å
r_factor	0.2081
r_work	0.2066
r_free	0.2361

fit	/app/data/saxs_computation/ri/9ris/9ris.fit
pddf	/app/data/pr_computation/ri/9ris/9ris.pr.out
profile	/app/data/saxs_computation/ri/9ris/9ris.dat

Crystal structure of human IDO1 in complex with iDeg-1

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