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9uz3

Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with D-Trp

Method: X-RAY DIFFRACTION D_max: 104.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uz3
deposition_date	2025-05-16
last_revision	2026-04-08
title	Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with D-Trp
keywords	HEM protein, Complex, 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	32.61 Å
rg_electron	32.32 Å
i0	102957000.00
molecular_weight	83995.0 kDa
excluded_volume	106350 Å³
envelope_volume	129840 Å³
shell_volume	34511 Å³
envelope_diameter	110.6 Å
shell_rg	38.03 Å
envelope_rg	32.08 Å
shape_rg	32.30 Å
total_rg	32.85 Å
total_atoms	5929
n_residues	745
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	104.2 Å
rg_real	32.79 Å
rg_real_error	0.91 Å
i0_real	1.0300e+08
i0_real_error	1.6670e+06
rg_reciprocal	32.72 Å
i0_reciprocal	103000000.0000
total_estimate	0.8112
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.8 Å
skewness	0.396
kurtosis	-0.595
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	41810000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Maltose/maltodextrin-binding periplasmic protein,Indoleamine 2,3-dioxygenase 2
formula_weight	86825.9 kDa
ec_number	1.13.11.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6073

MGSSHHHHHHENLYFQGMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTTAVPLSLESYHISEEYGFLLPDSLKELPDHYRPWMEIANKLPQLIDAHQLQAHVDKMPLLSCQFLKGHREQRLAHLVLSFLTMGYVWQEGEAQPAEVLPRNLALPFVEVSRNLGLPPILVHSDLVLTNWTKKDPDGFLEIGNLETIISFPGGESLHGFILVTALVEKEAVPGIKALVQATNAILQPNQEALLQALQRLRLSIQDITKTLGQMHDYVDPDIFYAGIRIFLSGWKDNPAMPAGLMYEGVSQEPLKYSGGSAAQSTVLHAFDEFLGIRHSKESGDFLYRMRDYMPPSHKAFIEDIHSAPSLRDYILSSGQDHLLTAYNQCVQALAELRSYHITMVTKYLITAAAKAKHGKPNHLPGPPQALKDRGTGGTAVMSFLKSVRDKTLESILHPRG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 branched

description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
formula_weight	342.3 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CYANIDE ION
formula_weight	26.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	D-TRYPTOPHAN
formula_weight	204.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	144

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6. Citations (1)

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length_a	197.834 Å
length_b	197.834 Å
length_c	94.086 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	2.500 Å
resolution_low	42.420 Å
r_factor	0.2412
r_work	0.2394
r_free	0.2745

fit	/app/data/saxs_computation/uz/9uz3/9uz3.fit
pddf	/app/data/pr_computation/uz/9uz3/9uz3.pr.out
profile	/app/data/saxs_computation/uz/9uz3/9uz3.dat