SAXSdb — 1py2

▼

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

Interleukin-2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;5-[2,3-DICHLORO-4-(5-{1-[2-(2-GUANIDINO-4-METHYL-PENTANOYLAMINO)-ACETYL]-PIPERIDIN-4-YL}-1-METHYL-1H-PYRAZOL-3-YL)-PHENOXYMETHYL]-FURAN-2-CARBOXYLIC ACID ; × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;5-[2,3-DICHLORO-4-(5-{1-[2-(2-GUANIDINO-4-METHYL-PENTANOYLAMINO)-ACETYL]-PIPERIDIN-4-YL}-1-METHYL-1H-PYRAZOL-3-YL)-PHENOXYMETHYL]-FURAN-2-CARBOXYLIC ACID ; × 1 ZINC ION × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	;5-[2,3-DICHLORO-4-(5-{1-[2-(2-GUANIDINO-4-METHYL-PENTANOYLAMINO)-ACETYL]-PIPERIDIN-4-YL}-1-METHYL-1H-PYRAZOL-3-YL)-PHENOXYMETHYL]-FURAN-2-CARBOXYLIC ACID ; × 1 ZINC ION × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	;5-[2,3-DICHLORO-4-(5-{1-[2-(2-GUANIDINO-4-METHYL-PENTANOYLAMINO)-ACETYL]-PIPERIDIN-4-YL}-1-METHYL-1H-PYRAZOL-3-YL)-PHENOXYMETHYL]-FURAN-2-CARBOXYLIC ACID ; × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	;5-[2,3-DICHLORO-4-(5-{1-[2-(2-GUANIDINO-4-METHYL-PENTANOYLAMINO)-ACETYL]-PIPERIDIN-4-YL}-1-METHYL-1H-PYRAZOL-3-YL)-PHENOXYMETHYL]-FURAN-2-CARBOXYLIC ACID ; × 1 ZINC ION × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	;5-[2,3-DICHLORO-4-(5-{1-[2-(2-GUANIDINO-4-METHYL-PENTANOYLAMINO)-ACETYL]-PIPERIDIN-4-YL}-1-METHYL-1H-PYRAZOL-3-YL)-PHENOXYMETHYL]-FURAN-2-CARBOXYLIC ACID ; × 1 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IL2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–132； UniProt 21–152 Author chain B； PDBConstruct 1–132； UniProt 21–152 Author chain C； PDBConstruct 1–132； UniProt 21–152 Author chain D； PDBConstruct 1–132； UniProt 21–152

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1py2
Deposition date deposition_date	2003-07-07
Structure title title	Structure of a 60 nM Small Molecule Bound to a Hot Spot on IL-2
Keywords keywords	IL-2, interleukin 2, small molecule, hot spot, molecular recognition, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1py2__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1py2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1py2__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	15.81 Å
Rg (electron density)	14.44 Å
Total Rg	15.74 Å
Atom count	1004
Residues	117
Excluded volume	18326 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1py2__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1py2__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1py2__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1py2__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1py2__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1py2__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Interleukin-2
Molecular weight formula_weight	15334.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4015

APTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNRWITFCQSIISTL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;5-[2,3-DICHLORO-4-(5-{1-[2-(2-GUANIDINO-4-METHYL-PENTANOYLAMINO)-ACETYL]-PIPERIDIN-4-YL}-1-METHYL-1H-PYRAZOL-3-YL)-PHENOXYMETHYL]-FURAN-2-CARBOXYLIC ACID ;
Molecular weight formula_weight	662.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1py2a_
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

Domain ID domain_id	d1py2b_
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

Domain ID domain_id	d1py2c_
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

Domain ID domain_id	d1py2d_
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 (4 domains)

Domain ID domain_id	1py2A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1py2B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1py2C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1py2D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	59.982 Å
Unit-cell length b length_b	52.448 Å
Unit-cell length c length_c	89.469 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2734
R_work r_work	0.2711
R_free r_free	0.3196

Structure of a 60 nM Small Molecule Bound to a Hot Spot on IL-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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1py2__assembly_1__model_1

1py2__assembly_1__model_1 | I(q)

1py2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of a 60 nM Small Molecule Bound to a Hot Spot on IL-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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1py2__assembly_1__model_1

1py2__assembly_1__model_1 | I(q)

1py2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)