SAXSdb — 8ywr

▼

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 42–212	Not recorded	Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2 × 2 Light chain of the Fab fragment of anti-IL-6 antibody 68F2 × 2 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

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 8YWR	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 construct 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 construct 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 construct 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 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 construct 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
4NI7 Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025) Deposited 2013-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 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, 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
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 ligand/ion 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 construct 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

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 1–171； UniProt 42–212

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8ywr
Deposition date deposition_date	2024-03-31
Structure title title	Crystal structure of the Fab fragment of the anti-IL-6 antibody 68F2 in complex with a domain-swapped IL-6 dimer
Keywords keywords	interleukin, dimer, swap, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.85 Å
Radius of gyration Rg (electron density) rg_electron	30.64 Å
Forward intensity I(0) i0	60656100.00
Molecular weight molecular_weight	60774.0 kDa
Excluded volume excluded_volume	75874 Å³
Envelope volume envelope_volume	106820 Å³
Hydration-shell volume shell_volume	30836 Å³
Envelope diameter envelope_diameter	107.3 Å
Shell Rg shell_rg	35.72 Å
Envelope Rg envelope_rg	31.12 Å
Shape Rg shape_rg	30.59 Å
Total Rg total_rg	31.27 Å
Total atoms total_atoms	4278
Residues n_residues	564
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	101.5 Å
Rg (real space) rg_real	31.06 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	6.0660e+07
I(0) uncertainty (real space) i0_real_error	9.9720e+05
Rg (reciprocal space) rg_reciprocal	30.98 Å
I(0) (reciprocal space) i0_reciprocal	60650000.0000
Solution quality estimate total_estimate	0.8680
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	99.5 Å
Skewness Skewness skewness	0.493
Kurtosis Kurtosis kurtosis	-0.347
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5632000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.882; Smooth: 0.856

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Interleukin-6
Molecular weight formula_weight	19670.5 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	4283

PHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM

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	Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2
Molecular weight formula_weight	23822.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLQESGPGLVKPSQTLSLTCTVSGGSITTRYYAWSWIRQPPGKGLEWMGVIDYDGDTYYSPSLKSRTSISWDTSKNQFSLQLSSVTPEDTAVYYCARDPDVVTGFHYDYWGQGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Lama glama

Entity 3 Entity 3 polymer

Description description	Light chain of the Fab fragment of anti-IL-6 antibody 68F2
Molecular weight formula_weight	22949.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

QAVLTQPPLVSGTPGQTVTISCAGANNDIGTYAYVSWYQQLPGTAPKLLIYKVTTRASGIPSRFSGSKSGNTASLTISGLQSEDEADYYCASYRNFNNAVFGRGTHLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Lama glama

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	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

▶

8. Citations (1)

▶

Unit-cell length a length_a	46.550 Å
Unit-cell length b length_b	92.860 Å
Unit-cell length c length_c	84.630 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	monoclinic

Resolution resolution	2.930 Å
Low-resolution limit resolution_low	41.070 Å
R factor r_factor	0.2183
R_work r_work	0.2142
R_free r_free	0.2556

fit	/app/data/saxs_computation/yw/8ywr/8ywr.fit
pddf	/app/data/pr_computation/yw/8ywr/8ywr.pr.out
profile	/app/data/saxs_computation/yw/8ywr/8ywr.dat

Crystal structure of the Fab fragment of the anti-IL-6 antibody 68F2 in complex with a domain-swapped IL-6 dimer

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 (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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)