SAXSdb — 21oo

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase I,Indoleamine 2,3-dioxygenase 2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–387	Mutation：H143Y	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 D0Q 5-methyl-L-tryptophan × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.55 Å R-free 0.228

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 21OO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
21OK Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) H143Y mutant complexed with 5-methoxy-L-Trp Deposited 2025-12-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–387（367 aa）	Mutation：H143Y	A1A2Y 5-methoxy-L-tryptophan × 1 EDO 1,2-ETHANEDIOL × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.60 Å R-free 0.315
21OM Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with 5-hydroxy-L-Trp Deposited 2025-12-22	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–387（367 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 4PQ 5-hydroxy-L-tryptophan × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.68 Å R-free 0.334

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0ABU7R6J9_9FLAO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–384； UniProt 21–387

DNA polymerase I,Indoleamine 2,3-dioxygenase 2

Homo sapiens

UniProt Q6ZQW0

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 10–407	Mutation：H143Y	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 D0Q 5-methyl-L-tryptophan × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.55 Å R-free 0.228

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 21OO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
21OK Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) H143Y mutant complexed with 5-methoxy-L-Trp Deposited 2025-12-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–407（398 aa）	Mutation：H143Y	A1A2Y 5-methoxy-L-tryptophan × 1 EDO 1,2-ETHANEDIOL × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.60 Å R-free 0.315
21OM Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with 5-hydroxy-L-Trp Deposited 2025-12-22	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–407（398 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 4PQ 5-hydroxy-L-tryptophan × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.68 Å R-free 0.334
9UYY Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with L-Trp Deposited 2025-05-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–407（398 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 5 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 TRP TRYPTOPHAN × 1 CYN CYANIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.25 Å R-free 0.300
9UYZ Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with 5-HT Deposited 2025-05-16	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–407（398 aa）	Not recorded	SRO SEROTONIN × 1 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.45 Å R-free 0.264
9UZ0 Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) as resting state Deposited 2025-05-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–407（398 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 CIT CITRIC ACID × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.45 Å R-free 0.248
9UZ1 Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) H143Y mutant complexed with L-Trp Deposited 2025-05-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–407（398 aa）	Mutation：H143Y	TRP TRYPTOPHAN × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.35 Å R-free 0.236
9UZ2 Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with Cyanide ion Deposited 2025-05-16	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–407（398 aa）	Not recorded	CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.55 Å R-free 0.238
9UZ3 Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with D-Trp Deposited 2025-05-16	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–407（398 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 DTR D-TRYPTOPHAN × 1 EDO 1,2-ETHANEDIOL × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.50 Å R-free 0.275
9UZ4 Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with 5-methoxy-L-Trp Deposited 2025-05-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–407（398 aa）	Not recorded	A1A2Y 5-methoxy-L-tryptophan × 1 EDO 1,2-ETHANEDIOL × 12 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.50 Å R-free 0.280
9UZ5 Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with 5-methyl-L-Trp Deposited 2025-05-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–407（398 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 D0Q 5-methyl-L-tryptophan × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；PEG 3350, Sodium citrate tribasic dihydrate	Resolution 2.50 Å R-free 0.229

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	I23O2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 385–782； UniProt 10–407

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	21oo
Deposition date deposition_date	2025-12-22
最后修订 last_revision	2026-04-08
Structure title title	Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) H143Y mutant complexed with 5-methyl-L-Trp
Keywords keywords	HEM protein, Complex, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.66 Å
Radius of gyration Rg (electron density) rg_electron	32.34 Å
Forward intensity I(0) i0	104461000.00
Molecular weight molecular_weight	84568.0 kDa
Excluded volume excluded_volume	107050 Å³
Envelope volume envelope_volume	131310 Å³
Hydration-shell volume shell_volume	34784 Å³
Envelope diameter envelope_diameter	111.9 Å
Shell Rg shell_rg	38.09 Å
Envelope Rg envelope_rg	32.19 Å
Shape Rg shape_rg	32.33 Å
Total Rg total_rg	32.88 Å
Total atoms total_atoms	5970
Residues n_residues	750
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	107.9 Å
Rg (real space) rg_real	32.84 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	1.0450e+08
I(0) uncertainty (real space) i0_real_error	1.6950e+06
Rg (reciprocal space) rg_reciprocal	32.77 Å
I(0) (reciprocal space) i0_reciprocal	104500000.0000
Solution quality estimate total_estimate	0.8689
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.2 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.594
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	43150000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.867; Smooth: 0.925

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	DNA polymerase I,Indoleamine 2,3-dioxygenase 2
Molecular weight formula_weight	86850.9 kDa
EC 编号 ec_number	2.7.7.7,1.13.11.-
Mutation mutation	H143Y
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6033

MGSSHHHHHHENLYFQGMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTTAVPLSLESYHISEEYGFLLPDSLKELPDHYRPWMEIANKLPQLIDAHQLQAHVDKMPLLSCQFLKGHREQRLAHLVLSFLTMGYVWQEGEAQPAEVLPRNLALPFVEVSRNLGLPPILVYSDLVLTNWTKKDPDGFLEIGNLETIISFPGGESLHGFILVTALVEKEAVPGIKALVQATNAILQPNQEALLQALQRLRLSIQDITKTLGQMHDYVDPDIFYAGIRIFLSGWKDNPAMPAGLMYEGVSQEPLKYSGGSAAQSTVLHAFDEFLGIRHSKESGDFLYRMRDYMPPSHKAFIEDIHSAPSLRDYILSSGQDHLLTAYNQCVQALAELRSYHITMVTKYLITAAAKAKHGKPNHLPGPPQALKDRGTGGTAVMSFLKSVRDKTLESILHPRG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CYANIDE ION
Molecular weight formula_weight	26.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	5-methyl-L-tryptophan
Molecular weight formula_weight	218.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	63

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8. Citations (1)

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Unit-cell length a length_a	199.106 Å
Unit-cell length b length_b	199.106 Å
Unit-cell length c length_c	94.456 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	49.100 Å
R factor r_factor	0.2044
R_work r_work	0.2032
R_free r_free	0.2281

fit	/app/data/saxs_computation/1o/21oo/21oo.fit
pddf	/app/data/pr_computation/1o/21oo/21oo.pr.out
profile	/app/data/saxs_computation/1o/21oo/21oo.dat

Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) H143Y mutant complexed with 5-methyl-L-Trp

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase I,Indoleamine 2,3-dioxygenase 2

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase I,Indoleamine 2,3-dioxygenase 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)