1nr4

High resolution crystal structures of thymus and activation-regulated chemokine

Method: X-RAY DIFFRACTION D_max: 120.4 Å Quality: GOOD

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

Thymus and activation-regulated chemokine

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 24–94 Chain B； UniProt 24–94	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；285 K；0.16M ammonium sulfate, 0.08M Sodium acetate, 20% PEG 4000, 15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.72 Å R-free 0.239
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 24–94 Chain D； UniProt 24–94	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；285 K；0.16M ammonium sulfate, 0.08M Sodium acetate, 20% PEG 4000, 15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.72 Å R-free 0.239
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 24–94 Chain F； UniProt 24–94	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；285 K；0.16M ammonium sulfate, 0.08M Sodium acetate, 20% PEG 4000, 15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.72 Å R-free 0.239
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 24–94 Chain H； UniProt 24–94	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；285 K；0.16M ammonium sulfate, 0.08M Sodium acetate, 20% PEG 4000, 15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.72 Å R-free 0.239
5	Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 24–94 Chain B； UniProt 24–94 Chain C； UniProt 24–94 Chain D； UniProt 24–94 Chain E； UniProt 24–94 Chain F； UniProt 24–94 Chain G； UniProt 24–94 Chain H； UniProt 24–94	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；285 K；0.16M ammonium sulfate, 0.08M Sodium acetate, 20% PEG 4000, 15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.72 Å R-free 0.239

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 1NR4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NR2 High resolution crystal structures of thymus and activation-regulated chemokine Deposited 2003-01-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–94（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；288 K；0.17M ammonium acetate, 0.085M trisodium citrate, 25.5% PEG 4000, 15% w/v glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.18 Å R-free 0.299
1NR2 High resolution crystal structures of thymus and activation-regulated chemokine Deposited 2003-01-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 24–94（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；288 K；0.17M ammonium acetate, 0.085M trisodium citrate, 25.5% PEG 4000, 15% w/v glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.18 Å R-free 0.299
5WK3 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CCL17 AND M116 FAB Deposited 2017-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 24–94（71 aa） Fragment：UNP residues 24-94	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；15% PEG 3350, 0.2 M POTASSIUM SODIUM TARTRATE	Resolution 1.90 Å R-free 0.231
5WK3 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CCL17 AND M116 FAB Deposited 2017-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 24–94（71 aa） Fragment：UNP residues 24-94	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；15% PEG 3350, 0.2 M POTASSIUM SODIUM TARTRATE	Resolution 1.90 Å R-free 0.231
5WK3 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CCL17 AND M116 FAB Deposited 2017-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 24–94（71 aa） Fragment：UNP residues 24-94	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；15% PEG 3350, 0.2 M POTASSIUM SODIUM TARTRATE	Resolution 1.90 Å R-free 0.231
5WK3 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CCL17 AND M116 FAB Deposited 2017-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 24–94（71 aa） Fragment：UNP residues 24-94	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；15% PEG 3350, 0.2 M POTASSIUM SODIUM TARTRATE	Resolution 1.90 Å R-free 0.231
7S4N Crystal structure of the tick evasin EVA-P974 complexed to human chemokine CCL17 Deposited 2021-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–94（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；291 K；0.1 M Na3 Cit 3.5 pH (Buffer) 3 M NaCl (Precipitant)	Resolution 1.65 Å R-free 0.237
7S4N Crystal structure of the tick evasin EVA-P974 complexed to human chemokine CCL17 Deposited 2021-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 24–94（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；291 K；0.1 M Na3 Cit 3.5 pH (Buffer) 3 M NaCl (Precipitant)	Resolution 1.65 Å R-free 0.237
7SCV Crystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Human Chemokine CCL17 Deposited 2021-09-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–94（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Na Acet 4.6 pH (Buffer),2 M NaCl (Precipitant)	Resolution 2.01 Å R-free 0.251
8FJ2 Crystal Structure of the Tick Evasin EVA-AAM1001(C8) Complexed to Human Chemokine CCL17 Deposited 2022-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–94（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4.3 M NaCl, 0.1 M HEPES pH 7.4	Resolution 2.07 Å R-free 0.231
8FJ2 Crystal Structure of the Tick Evasin EVA-AAM1001(C8) Complexed to Human Chemokine CCL17 Deposited 2022-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–94（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；4.3 M NaCl, 0.1 M HEPES pH 7.4	Resolution 2.07 Å R-free 0.231
8SKK Crystal Structure of the Tick Evasin EVA-AAM1001(L39P) Complexed to Human Chemokine CCL17 Deposited 2023-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–94（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2M Ammonium sulfate, 0.1 M HEPES pH 7.0	Resolution 2.10 Å R-free 0.211

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CCL17_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–71； UniProt 24–94 Author chain B； PDBConstruct 1–71； UniProt 24–94 Author chain C； PDBConstruct 1–71； UniProt 24–94 Author chain D； PDBConstruct 1–71； UniProt 24–94 Author chain E； PDBConstruct 1–71； UniProt 24–94 Author chain F； PDBConstruct 1–71； UniProt 24–94 Author chain G； PDBConstruct 1–71； UniProt 24–94 Author chain H； PDBConstruct 1–71； UniProt 24–94

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1nr4
Deposition date deposition_date	2003-01-23
Structure title title	High resolution crystal structures of thymus and activation-regulated chemokine
Keywords keywords	TARC, chemokine, cytokine, CC-chemokine, chemotaxis; CYTOKINE
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	35.52 Å
Radius of gyration Rg (electron density) rg_electron	35.17 Å
Forward intensity I(0) i0	63118900.00
Molecular weight molecular_weight	60659.0 kDa
Excluded volume excluded_volume	75305 Å³
Envelope volume envelope_volume	114180 Å³
Hydration-shell volume shell_volume	29696 Å³
Envelope diameter envelope_diameter	128.6 Å
Shell Rg shell_rg	37.82 Å
Envelope Rg envelope_rg	34.38 Å
Shape Rg shape_rg	35.12 Å
Total Rg total_rg	35.55 Å
Total atoms total_atoms	4235
Residues n_residues	524
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	120.4 Å
Rg (real space) rg_real	35.70 Å
Rg uncertainty (real space) rg_real_error	1.42 Å
I(0) (real space) i0_real	6.3120e+07
I(0) uncertainty (real space) i0_real_error	1.0940e+06
Rg (reciprocal space) rg_reciprocal	35.59 Å
I(0) (reciprocal space) i0_reciprocal	63110000.0000
Solution quality estimate total_estimate	0.8586
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	45.5 Å
Skewness Skewness skewness	0.311
Kurtosis Kurtosis kurtosis	-0.616
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4031000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.745; Smooth: 0.893

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1nr4a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1nr4b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1nr4c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1nr4d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1nr4e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1nr4f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1nr4g_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1nr4h_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (8 domains)

Domain ID domain_id	1nr4A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1nr4B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1nr4C00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1nr4D00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1nr4E00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1nr4F00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1nr4G00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1nr4H00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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8. Citations (2)

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Unit-cell length a length_a	44.350 Å
Unit-cell length b length_b	56.525 Å
Unit-cell length c length_c	76.616 Å
Unit-cell angle α angle_alpha	69.97 °
Unit-cell angle β angle_beta	85.56 °
Unit-cell angle γ angle_gamma	72.74 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.720 Å
Low-resolution limit resolution_low	24.920 Å
R factor r_factor	0.2011
R_work r_work	0.1992
R_free r_free	0.2390

Description description	Thymus and activation-regulated chemokine
Molecular weight formula_weight	8096.3 kDa
Source method src_method	syn
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	4882

High resolution crystal structures of thymus and activation-regulated chemokine

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

Thymus and activation-regulated chemokine

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	647

fit	/app/data/saxs_computation/nr/1nr4/1nr4.fit
pddf	/app/data/pr_computation/nr/1nr4/1nr4.pr.out
profile	/app/data/saxs_computation/nr/1nr4/1nr4.dat