SAXSdb — 4ni7

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

Interleukin-6

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–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 28–212	Not recorded	SOMAmer SL1025 × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；31% PEG 3350, 180 mM LiNO3, 100 mM Sodium Acetate (pH 5.5), 2.5% Hexamine Cobalt Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.40 Å R-free 0.260

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 4NI7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ALU HUMAN INTERLEUKIN-6 Deposited 1997-06-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–212（185 aa）	Not recorded	SO4 SULFATE ION × 8 TLA L(+)-TARTARIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.3；PROTEIN AT 15 MG/ML WAS CRYSTALLIZED FROM 1.8M AMMONIUM SULFATE, 300 MM SODIUM POTASSIUM TARTRATE, IN 100MM PH 6.3 SODIUM CITRATE BUFFER.	Resolution 1.90 Å R-free 0.277
1ALU HUMAN INTERLEUKIN-6 Deposited 1997-06-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–212（185 aa）	Not recorded	SO4 SULFATE ION × 8 TLA L(+)-TARTARIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.3；PROTEIN AT 15 MG/ML WAS CRYSTALLIZED FROM 1.8M AMMONIUM SULFATE, 300 MM SODIUM POTASSIUM TARTRATE, IN 100MM PH 6.3 SODIUM CITRATE BUFFER.	Resolution 1.90 Å R-free 0.277
1IL6 HUMAN INTERLEUKIN-6, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-01-31	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–212（185 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K	Resolution not provided
1P9M Crystal structure of the hexameric human IL-6/IL-6 alpha receptor/gp130 complex Deposited 2003-05-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 29–212（184 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；Sodium formate, Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.65 Å R-free 0.334
2IL6 HUMAN INTERLEUKIN-6, NMR, 32 STRUCTURES Deposited 1997-01-31	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–212（185 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K	Resolution not provided
4CNI Crystal structure of the Fab portion of Olokizumab in complex with IL- 6 Deposited 2014-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 42–212（171 aa） Fragment：RESIDUES 41-212	Not recorded	TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.215
4CNI Crystal structure of the Fab portion of Olokizumab in complex with IL- 6 Deposited 2014-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 42–212（171 aa） Fragment：RESIDUES 41-212	Not recorded	TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.215
4J4L Modular evolution and design of the protein binding interface Deposited 2013-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 47–212（166 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；290 K；0.1M magnesium formate, 15-18% w/v polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, temperature 290K	Resolution 2.30 Å R-free 0.268
4J4L Modular evolution and design of the protein binding interface Deposited 2013-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 47–212（166 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；290 K；0.1M magnesium formate, 15-18% w/v polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, temperature 290K	Resolution 2.30 Å R-free 0.268
4NI9 Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025), FORM 2 Deposited 2013-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 28–212（185 aa） Chain C 28–212（185 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；31% PEG 3350, 90 mM Magnesium Sulfate, 90 mM Sodium Acetate (pH 5.5) 100 mM LiCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.55 Å R-free 0.239
4O9H Structure of Interleukin-6 in complex with a Camelid Fab fragment Deposited 2014-01-02	Different construct 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 28–212（185 aa） Fragment：UNP residues 28-212	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；277 K；2M Ammonium sulfate, 0.15M Na citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.42 Å R-free 0.244
4ZS7 Structural mimicry of receptor interaction by antagonistic IL-6 antibodies Deposited 2015-05-13	Different construct 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 42–212（171 aa） Fragment：residues 14-184	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25% PEG 4K, 0.15 M (NH4)2SO4, 0.1 M MES pH 5.5. Took 9 month	Resolution 2.93 Å R-free 0.293
5FUC Biophysical and cellular characterisation of a junctional epitope antibody that locks IL-6 and gp80 together in a stable complex: implications for new therapeutic strategies Deposited 2016-01-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 49–212（164 aa） Fragment：RESIDUES 49-212	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M MES, PH 6.5, 14% PEG20K	Resolution 2.70 Å R-free 0.287
5FUC Biophysical and cellular characterisation of a junctional epitope antibody that locks IL-6 and gp80 together in a stable complex: implications for new therapeutic strategies Deposited 2016-01-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 49–212（164 aa） Fragment：RESIDUES 49-212	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M MES, PH 6.5, 14% PEG20K	Resolution 2.70 Å R-free 0.287
7NXZ Synthetic glycoform of Human Interleukin 6 Deposited 2021-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 30–212（183 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2-0.25 M sodium malonate, pH 7.0 and 18-22% (w/v) PEG 3350	Resolution 2.00 Å R-free 0.253
8D82 Cryo-EM structure of human IL-6 signaling complex in detergent: model containing full extracellular domains Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 30–212（183 aa） Chain H 30–212（183 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
8QY5 Structure of interleukin 6. Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–212（212 aa） Chain E 1–212（212 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QY6 Structure of interleukin 6 (gp130 P496L mutant). Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–212（212 aa） Chain E 1–212（212 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
8YWQ Crystal structure of the Fab fragment of the anti-IL-6 antibody I9H in complex with a domain-swapped IL-6 dimer Deposited 2024-03-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 28–212（185 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；40% v/v 2-methyl-2,4-pentanediol, 100 mM CAPS (seed stock crystallization conditions: 14-16% PEG 8000, 100 mM magnesium acetate, 100 mM MES pH 6.5)	Resolution 2.51 Å R-free 0.277
8YWR Crystal structure of the Fab fragment of the anti-IL-6 antibody 68F2 in complex with a domain-swapped IL-6 dimer Deposited 2024-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 42–212（171 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25% PEG 4K, 0.15 M (NH4)2SO4, 0.1 M MES	Resolution 2.93 Å R-free 0.256

16 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IL6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–186； UniProt 28–212

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	4ni7
Deposition date deposition_date	2013-11-05
Structure title title	Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025)
Keywords keywords	Interleukin-6, CYTOKINE-DNA complex; CYTOKINE/DNA
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	19.71 Å
Radius of gyration Rg (electron density) rg_electron	18.33 Å
Forward intensity I(0) i0	18742000.00
Molecular weight molecular_weight	26964.0 kDa
Excluded volume excluded_volume	31150 Å³
Envelope volume envelope_volume	38692 Å³
Hydration-shell volume shell_volume	17981 Å³
Envelope diameter envelope_diameter	62.5 Å
Shell Rg shell_rg	24.21 Å
Envelope Rg envelope_rg	18.52 Å
Shape Rg shape_rg	18.26 Å
Total Rg total_rg	19.25 Å
Total atoms total_atoms	1861
Residues n_residues	167
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	61.1 Å
Rg (real space) rg_real	19.58 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.8740e+07
I(0) uncertainty (real space) i0_real_error	2.3520e+05
Rg (reciprocal space) rg_reciprocal	19.60 Å
I(0) (reciprocal space) i0_reciprocal	18740000.0000
Solution quality estimate total_estimate	0.9103
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.076
Kurtosis Kurtosis kurtosis	-0.582
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1982000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Interleukin-6
Molecular weight formula_weight	21137.2 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	1890

MAPVPPGEDSKDVAAPHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM

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 polymer

Description description	SOMAmer SL1025
Molecular weight formula_weight	11402.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

GGCAGGXXXGGXAXXAACACGXXAAGXCGXGG

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4ni7a_
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.26.1.1 — Long-chain cytokines

CATH v4.4 (1 domains)

Domain ID domain_id	4ni7A00
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	50.230 Å
Unit-cell length b length_b	50.230 Å
Unit-cell length c length_c	103.630 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	3

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	43.500 Å
R factor r_factor	0.2240
R_work r_work	0.2220
R_free r_free	0.2600

fit	/app/data/saxs_computation/ni/4ni7/4ni7.fit
pddf	/app/data/pr_computation/ni/4ni7/4ni7.pr.out
profile	/app/data/saxs_computation/ni/4ni7/4ni7.dat

Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025)

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

Interleukin-6

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)