SAXSdb — 4nem

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

Interleukin-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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 4–133	Not recorded	2JY 5-[(2,3-dichlorophenoxy)methyl]furan-2-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；34% PEG 8K, 0.1 M NaOAc, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.93 Å R-free 0.259

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 4NEM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NEJ Small molecular fragment bound to crystal contact interface of Interleukin-2 Deposited 2013-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–133（130 aa）	Not recorded	2K1 5-methylfuran-2-carboxylic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；34% PEG 8K, 0.1 M NaOAc, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.92 Å R-free 0.258
6VWU X-ray structure of ALKS 4230, a fusion of circularly permuted human Interleukin-2 and Interleukin-2 Receptor alpha Deposited 2020-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 75–133（59 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；An equal volume of protein was mixed with crystallization buffer, 25 % (w/v) PEG 3350, 0.2 M MgCl2, 0.1 M Hepes 7.5. Large crystals appeared within 48-72 hours, and were frozen in a cryoprotectant consisting of mother liquor with 10 % glycerol	Resolution 3.40 Å R-free 0.297

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

View Construct and Data Evidence

UniProt name	Q6QWN0_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–130； UniProt 4–133

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	4nem
Deposition date deposition_date	2013-10-29
Structure title title	Small molecular fragment bound to crystal contact interface of Interleukin-2
Keywords keywords	fragment mapping, crystal contact, cytokine, Interleukin-2, helixbundle, CD25, extracellular, IMMUNE SYSTEM; IMMUNE SYSTEM
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	15.57 Å
Radius of gyration Rg (electron density) rg_electron	14.29 Å
Forward intensity I(0) i0	3321000.00
Molecular weight molecular_weight	13615.0 kDa
Excluded volume excluded_volume	17412 Å³
Envelope volume envelope_volume	19546 Å³
Hydration-shell volume shell_volume	11849 Å³
Envelope diameter envelope_diameter	52.4 Å
Shell Rg shell_rg	19.82 Å
Envelope Rg envelope_rg	14.79 Å
Shape Rg shape_rg	14.24 Å
Total Rg total_rg	15.63 Å
Total atoms total_atoms	953
Residues n_residues	114
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	52.8 Å
Rg (real space) rg_real	15.51 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	3.3210e+06
I(0) uncertainty (real space) i0_real_error	3.6550e+04
Rg (reciprocal space) rg_reciprocal	15.51 Å
I(0) (reciprocal space) i0_reciprocal	3321000.0000
Solution quality estimate total_estimate	0.8693
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.226
Kurtosis Kurtosis kurtosis	-0.241
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	500000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Interleukin-2
Molecular weight formula_weight	15150.6 kDa
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	968

SSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNRWITFSQSIISTLT

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

Entity 2 Entity 2 non-polymer

Description description	5-[(2,3-dichlorophenoxy)methyl]furan-2-carboxylic acid
Molecular weight formula_weight	287.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4nema_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

CATH v4.4 (1 domains)

Domain ID domain_id	4nemA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	31.709 Å
Unit-cell length b length_b	48.544 Å
Unit-cell length c length_c	79.767 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.934 Å
Low-resolution limit resolution_low	41.468 Å
R factor r_factor	0.2093
R_work r_work	0.2069
R_free r_free	0.2589

fit	/app/data/saxs_computation/ne/4nem/4nem.fit
pddf	/app/data/pr_computation/ne/4nem/4nem.pr.out
profile	/app/data/saxs_computation/ne/4nem/4nem.dat

Small molecular fragment bound to crystal contact interface of Interleukin-2

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

Interleukin-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