SAXSdb — 2xqb

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

INTERLEUKIN 15

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 49–162	Not recorded	ANTI-IL-15 ANTIBODY × 1 ANTI-IL-15 ANTIBODY × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9.5；PCTP 100MM, PH 9.5, 25 %W/V PEG-3350, 200MM AMMONIUM SULPHATE	Resolution 2.60 Å R-free 0.318

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 2XQB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2Z3Q Crystal structure of the IL-15/IL-15Ra complex Deposited 2007-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 49–162（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.85 Å R-free 0.252
2Z3Q Crystal structure of the IL-15/IL-15Ra complex Deposited 2007-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 49–162（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.85 Å R-free 0.252
2Z3R Crystal structure of the IL-15/IL-15Ra complex Deposited 2007-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 49–162（114 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.250
2Z3R Crystal structure of the IL-15/IL-15Ra complex Deposited 2007-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 49–162（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.250
2Z3R Crystal structure of the IL-15/IL-15Ra complex Deposited 2007-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 49–162（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.250
2Z3R Crystal structure of the IL-15/IL-15Ra complex Deposited 2007-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 49–162（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.250
2Z3R Crystal structure of the IL-15/IL-15Ra complex Deposited 2007-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 49–162（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.250
2Z3R Crystal structure of the IL-15/IL-15Ra complex Deposited 2007-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 49–162（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.250
2Z3R Crystal structure of the IL-15/IL-15Ra complex Deposited 2007-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 49–162（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.250
2Z3R Crystal structure of the IL-15/IL-15Ra complex Deposited 2007-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 49–162（114 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.250
4GS7 Structure of the Interleukin-15 quaternary complex Deposited 2012-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 49–162（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.75；298 K；22.5% PEG3350, 0.1M BIS-TRIS propane, 0.2M sodium acetate, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.35 Å R-free 0.227

3 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IL15_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–114； UniProt 49–162

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	2xqb
Deposition date deposition_date	2010-09-01
Structure title title	Crystal Structure of anti-IL-15 Antibody in Complex with human IL-15
Keywords keywords	IMMUNE SYSTEM, AFFINITY MATURATION; 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	28.27 Å
Radius of gyration Rg (electron density) rg_electron	27.85 Å
Forward intensity I(0) i0	54252900.00
Molecular weight molecular_weight	56828.0 kDa
Excluded volume excluded_volume	70650 Å³
Envelope volume envelope_volume	88345 Å³
Hydration-shell volume shell_volume	27852 Å³
Envelope diameter envelope_diameter	98.7 Å
Shell Rg shell_rg	33.70 Å
Envelope Rg envelope_rg	27.65 Å
Shape Rg shape_rg	27.82 Å
Total Rg total_rg	28.53 Å
Total atoms total_atoms	3997
Residues n_residues	520
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	95.8 Å
Rg (real space) rg_real	28.47 Å
Rg uncertainty (real space) rg_real_error	1.03 Å
I(0) (real space) i0_real	5.4250e+07
I(0) uncertainty (real space) i0_real_error	9.8180e+05
Rg (reciprocal space) rg_reciprocal	28.41 Å
I(0) (reciprocal space) i0_reciprocal	54250000.0000
Solution quality estimate total_estimate	0.8643
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.496
Kurtosis Kurtosis kurtosis	-0.291
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10740000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.958

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	INTERLEUKIN 15
Molecular weight formula_weight	12784.5 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	4063

NWVNVISDLKKIEDLIQSMHIDATLYTESDVHPSCKVTAMKCFLLELQVISLESGDASIHDTVENLIILANNSLSSNGNVTESGCKECEELEEKNIKEFLQSFVHIVQMFINTS

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 polymer

Description description	ANTI-IL-15 ANTIBODY
Molecular weight formula_weight	25390.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLVQSGAEVKKPGASVKVSCKASGYSFSSFGISWVRQAPGQGLEWLGWISAFNGYTKYAQKFQDRVTMTTDTSTSTAYMELRSLRSDDTAVYYCARDPAAWPLQQSLAWFDPWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHQYVL

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	Homo sapiens

Entity 3 Entity 3 polymer

Description description	ANTI-IL-15 ANTIBODY
Molecular weight formula_weight	22915.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

TQPPSASGTPGQRVTISCSGSTSNLKRNYVYWYQQLPGTAPKLLIYRDRRRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCAWYDRELSEWVFGGGTKLTVLQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2xqba_
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	d2xqbh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2xqbl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2xqbl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id	2xqbA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	70 — Interleukin-15/Interleukin-21

Domain ID domain_id	2xqbH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2xqbH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2xqbL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2xqbL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	185.186 Å
Unit-cell length b length_b	43.754 Å
Unit-cell length c length_c	70.087 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.95 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	69.710 Å
R factor r_factor	0.2481
R_work r_work	0.2444
R_free r_free	0.3181

fit	/app/data/saxs_computation/xq/2xqb/2xqb.fit
pddf	/app/data/pr_computation/xq/2xqb/2xqb.pr.out
profile	/app/data/saxs_computation/xq/2xqb/2xqb.dat

Crystal Structure of anti-IL-15 Antibody in Complex with human IL-15

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

INTERLEUKIN 15

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)