9od7

Structure of disulfide-stabilized IL-18 variant

Method: X-RAY DIFFRACTION D_max: 53.7 Å Quality: GOOD

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

Interleukin-18

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 37–193	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；273.15 K；0.1M MIB buffer (mixing sodium malonate, imidazole, and boric acid in the molar ratios 2:3:3), pH 4.0, 25% PEG 1500	Resolution 1.90 Å R-free 0.195

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 9OD7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1J0S Solution structure of the human interleukin-18 Deposited 2002-11-21	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 37–193（157 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 150mM KCl；Pressure ambient NMR sample composition 1mM interleukin-18 U-15N,13C; 50mM phosphate buffer K \| 90% H2O/10% D2O	Resolution not provided
2VXT Crystal structure of human IL-18 complexed to murine reference antibody 125-2H Fab Deposited 2008-07-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 37–193（157 aa）	Mutation：YES	CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；IL-18 AND 125-2H FAB WERE MIXED (1:3 MASS RATIO), INCUBATED OVERNIGHT AT 277 K, PURIFIED BY MONOQ ANION EXCHANGE CHROMATOGRAPHY, AND CONCENTRATED TO 10 MG/ML. THE COMPLEX WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION BY MIXING COMPLEX (1.5 MICROLITERS [UL]) WITH 1.8 UL OF RESERVOIR SOLUTION (30% PEG 4000, 100 MM TRIS, PH 8.5, 0.2 M MGCL2) AND 0.3 UL OF 300 MM SULFO-BETAINE 201, AND SUSPENDING THE DROP OVER THE RESERVOIR AT 291 K. ROD-LIKE CRYSTALS APPEARED WITHIN ONE WEEK.	Resolution 1.49 Å R-free 0.196
3F62 Crystal Structure of Human IL-18 in complex with Ectromelia virus IL-18 Binding Protein Deposited 2008-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 37–193（157 aa） Fragment：UNP residues 37-193	Mutation：C38S, C68S, C76S, C127S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；30% Peg 3350, 0.5M KCl, 0.1M Sodium Citrate, pH 4.5, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 2.00 Å R-free 0.235
3WO2 Crystal structure of human interleukin-18 Deposited 2013-12-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 37–193（157 aa）	Not recorded	CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100mM Bis-Tris-HCl, 2.5M ammonium sulfate, 0.2%(w/v) CHAPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.33 Å R-free 0.271
3WO2 Crystal structure of human interleukin-18 Deposited 2013-12-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 37–193（157 aa）	Not recorded	CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100mM Bis-Tris-HCl, 2.5M ammonium sulfate, 0.2%(w/v) CHAPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.33 Å R-free 0.271
3WO2 Crystal structure of human interleukin-18 Deposited 2013-12-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 37–193（157 aa）	Not recorded	CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100mM Bis-Tris-HCl, 2.5M ammonium sulfate, 0.2%(w/v) CHAPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.33 Å R-free 0.271
3WO2 Crystal structure of human interleukin-18 Deposited 2013-12-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 37–193（157 aa）	Not recorded	CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100mM Bis-Tris-HCl, 2.5M ammonium sulfate, 0.2%(w/v) CHAPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.33 Å R-free 0.271
3WO3 Crystal structure of IL-18 in complex with IL-18 receptor alpha Deposited 2013-12-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 37–193（157 aa）	Not recorded	SO4 SULFATE ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；50mM N-Cyclohexyl-3-aminopropanesulfonic acid, 35% pentaerythritol ethoxylate (15/4 EO/OH), 350mM ammonium sulfate, 50mM LysoFos Choline 10, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.10 Å R-free 0.222
3WO3 Crystal structure of IL-18 in complex with IL-18 receptor alpha Deposited 2013-12-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 37–193（157 aa）	Not recorded	SO4 SULFATE ION × 12 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；50mM N-Cyclohexyl-3-aminopropanesulfonic acid, 35% pentaerythritol ethoxylate (15/4 EO/OH), 350mM ammonium sulfate, 50mM LysoFos Choline 10, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.10 Å R-free 0.222
3WO3 Crystal structure of IL-18 in complex with IL-18 receptor alpha Deposited 2013-12-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 37–193（157 aa）	Not recorded	SO4 SULFATE ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；50mM N-Cyclohexyl-3-aminopropanesulfonic acid, 35% pentaerythritol ethoxylate (15/4 EO/OH), 350mM ammonium sulfate, 50mM LysoFos Choline 10, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.10 Å R-free 0.222
3WO3 Crystal structure of IL-18 in complex with IL-18 receptor alpha Deposited 2013-12-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 37–193（157 aa）	Not recorded	SO4 SULFATE ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；50mM N-Cyclohexyl-3-aminopropanesulfonic acid, 35% pentaerythritol ethoxylate (15/4 EO/OH), 350mM ammonium sulfate, 50mM LysoFos Choline 10, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.10 Å R-free 0.222
3WO3 Crystal structure of IL-18 in complex with IL-18 receptor alpha Deposited 2013-12-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 37–193（157 aa）	Not recorded	SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；50mM N-Cyclohexyl-3-aminopropanesulfonic acid, 35% pentaerythritol ethoxylate (15/4 EO/OH), 350mM ammonium sulfate, 50mM LysoFos Choline 10, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.10 Å R-free 0.222
3WO3 Crystal structure of IL-18 in complex with IL-18 receptor alpha Deposited 2013-12-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 37–193（157 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；50mM N-Cyclohexyl-3-aminopropanesulfonic acid, 35% pentaerythritol ethoxylate (15/4 EO/OH), 350mM ammonium sulfate, 50mM LysoFos Choline 10, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.10 Å R-free 0.222
3WO4 Crystal structure of the IL-18 signaling ternary complex Deposited 2013-12-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 37–193（157 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；100mM Tris-HCl, 18% polyethylene glycol 4000, 200mM magnesium chloride, 40mM hexaamminecobalt (III) chloride, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.232
4EEE Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex with Human IL-18 Deposited 2012-03-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 37–193（157 aa） Chain D 37–193（157 aa）	Mutation：C38S, K67A, C68S, E69A, K70A, I71A, C76S, C127S Mutation：C38S, K67A, C68S, E69A, K70A, I71A, C76S, C127S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；18% PEG 3350, 0.1M BIS-TRIS PROPANE/CITRIC ACID PH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.71 Å R-free 0.270
4EKX Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex with Human IL-18 Deposited 2012-04-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 37–193（157 aa） Chain D 37–193（157 aa）	Mutation：C38S, K67A, C68S, E69A, K70A, I71A, C76S, C127S Mutation：C38S, K67A, C68S, E69A, K70A, I71A, C76S, C127S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；12% PEG 3350, pH 8.0, vapor diffusion, temperature 298K	Resolution 1.75 Å R-free 0.231
4EKX Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex with Human IL-18 Deposited 2012-04-10	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 37–193（157 aa）	Mutation：C38S, K67A, C68S, E69A, K70A, I71A, C76S, C127S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；12% PEG 3350, pH 8.0, vapor diffusion, temperature 298K	Resolution 1.75 Å R-free 0.231
4EKX Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex with Human IL-18 Deposited 2012-04-10	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 37–193（157 aa）	Mutation：C38S, K67A, C68S, E69A, K70A, I71A, C76S, C127S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；12% PEG 3350, pH 8.0, vapor diffusion, temperature 298K	Resolution 1.75 Å R-free 0.231
4HJJ Structure Reveals Function of the Dual Variable Domain Immunoglobulin (DVD-Ig) Molecule Deposited 2012-10-12	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 37–192（156 aa） Fragment：UNP resiudes 37-192	Not recorded	GOL GLYCEROL × 2 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；2M Ammonium Sulfate, 0.1M Sodium Acetate., pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.220
4R6U IL-18 receptor complex Deposited 2014-08-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 37–193（157 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；20% PEG3350, 0.03 M citric acid, 0.07 M Bis-Tris propane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.282
4R6U IL-18 receptor complex Deposited 2014-08-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 37–193（157 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；20% PEG3350, 0.03 M citric acid, 0.07 M Bis-Tris propane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.282
4XFS Structure of IL-18 SER Mutant I Deposited 2014-12-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 37–193（157 aa）	Mutation：K139A, K140A, E141A, E143A, L144A	DMS DIMETHYL SULFOXIDE × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；47% PEG 2K MME, 0.1M HEPES, 5% DMSO	Resolution 1.91 Å R-free 0.229
4XFS Structure of IL-18 SER Mutant I Deposited 2014-12-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 37–193（157 aa）	Mutation：K139A, K140A, E141A, E143A, L144A	DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；47% PEG 2K MME, 0.1M HEPES, 5% DMSO	Resolution 1.91 Å R-free 0.229
4XFS Structure of IL-18 SER Mutant I Deposited 2014-12-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 37–193（157 aa） Chain B 37–193（157 aa）	Mutation：K139A, K140A, E141A, E143A, L144A Mutation：K139A, K140A, E141A, E143A, L144A	DMS DIMETHYL SULFOXIDE × 5 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；47% PEG 2K MME, 0.1M HEPES, 5% DMSO	Resolution 1.91 Å R-free 0.229
4XFT Structure of IL-18 SER Mutant III Deposited 2014-12-29	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 37–193（157 aa）	Mutation：K67A, E69A, K70A, I71A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；35% PEG 3350, 0.1M MES, 5% DMSO	Resolution 2.00 Å R-free 0.218
4XFT Structure of IL-18 SER Mutant III Deposited 2014-12-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 37–193（157 aa）	Mutation：K67A, E69A, K70A, I71A	DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；35% PEG 3350, 0.1M MES, 5% DMSO	Resolution 2.00 Å R-free 0.218
4XFT Structure of IL-18 SER Mutant III Deposited 2014-12-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 37–193（157 aa） Chain B 37–193（157 aa）	Mutation：K67A, E69A, K70A, I71A Mutation：K67A, E69A, K70A, I71A	DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；35% PEG 3350, 0.1M MES, 5% DMSO	Resolution 2.00 Å R-free 0.218
4XFU Structure of IL-18 SER Mutant V Deposited 2014-12-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–189（157 aa）	Mutation：P57R, K67A, E69A, K70A, I71A, S105R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；35% PEG 3350, 0.1M Tris, 0.1M Sodium Acetate	Resolution 2.85 Å R-free 0.287
4XFU Structure of IL-18 SER Mutant V Deposited 2014-12-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 33–189（157 aa）	Mutation：P57R, K67A, E69A, K70A, I71A, S105R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；35% PEG 3350, 0.1M Tris, 0.1M Sodium Acetate	Resolution 2.85 Å R-free 0.287
4XFU Structure of IL-18 SER Mutant V Deposited 2014-12-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 33–189（157 aa） Chain B 33–189（157 aa）	Mutation：P57R, K67A, E69A, K70A, I71A, S105R Mutation：P57R, K67A, E69A, K70A, I71A, S105R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；35% PEG 3350, 0.1M Tris, 0.1M Sodium Acetate	Resolution 2.85 Å R-free 0.287
7AL7 The Crystal Structure of Human IL-18 in Complex With Human IL-18 Binding Protein Deposited 2020-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 36–193（158 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8000	Resolution 1.80 Å R-free 0.232
8J6K Crystal structure of pro-interleukin-18 and caspase-4 complex Deposited 2023-04-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–193（193 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Calcium acetate, 0.1M Tris-HCl pH 9.0, 13% PEG 8000, 0.01 M L-Glutathione reduced, 0.01 M L-Glutathione oxidized	Resolution 3.12 Å R-free 0.269
8SPB Caspase-4/Pro-IL-18 complex Deposited 2023-05-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 6–193（188 aa） Chain c 6–193（188 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8SV1 Caspase-1 complex with interleukin-18 Deposited 2023-05-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 6–193（188 aa） Chain c 6–193（188 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8URV Solution NMR structure of pro-IL-18 Deposited 2023-10-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–193（193 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298.1 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR measurement conditions pH 6.1；298.1 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.5 mM [U-13C; U-15N] pro-interleukin-18, 20 mM MES, 50 mM potassium chloride, 10 mM DTT, 97% H2O/3% D2O \| 97% H2O/3% D2O NMR sample composition 0.5 mM [U-13C; U-15N] pro-interleukin-18, 20 mM MES, 50 mM potassium chloride, 10 mM DTT, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [5% U-13C; U-15N] pro-interleukin-18, 20 mM MES, 50 mM potassium chloride, 10 mM DTT, 97% H2O/3% D2O \| 97% H2O/3% D2O	Resolution not provided
9OD9 Structure of disulfide-stabilized IL-18 variant Deposited 2025-04-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 37–193（157 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1M sodium citrate, pH 5.0, 20% PEG 600	Resolution 1.60 Å R-free 0.188

19 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IL18_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–157； UniProt 37–193

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9od7
Deposition date deposition_date	2025-04-25
最后修订 last_revision	2025-07-30
Structure title title	Structure of disulfide-stabilized IL-18 variant
Keywords keywords	protein structure, CYTOKINE; CYTOKINE
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	16.65 Å
Radius of gyration Rg (electron density) rg_electron	15.18 Å
Forward intensity I(0) i0	6533740.00
Molecular weight molecular_weight	18153.0 kDa
Excluded volume excluded_volume	22592 Å³
Envelope volume envelope_volume	26143 Å³
Hydration-shell volume shell_volume	14428 Å³
Envelope diameter envelope_diameter	53.0 Å
Shell Rg shell_rg	21.19 Å
Envelope Rg envelope_rg	15.56 Å
Shape Rg shape_rg	15.16 Å
Total Rg total_rg	16.36 Å
Total atoms total_atoms	1273
Residues n_residues	158
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	53.7 Å
Rg (real space) rg_real	16.54 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	6.5340e+06
I(0) uncertainty (real space) i0_real_error	7.4680e+04
Rg (reciprocal space) rg_reciprocal	16.55 Å
I(0) (reciprocal space) i0_reciprocal	6534000.0000
Solution quality estimate total_estimate	0.8066
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	53.0 Å
Skewness Skewness skewness	0.120
Kurtosis Kurtosis kurtosis	-0.330
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1213000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	70.916 Å
Unit-cell length b length_b	70.916 Å
Unit-cell length c length_c	89.904 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	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	hexagonal

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	36.270 Å
R factor r_factor	0.1593
R_work r_work	0.1575
R_free r_free	0.1954

Description description	Interleukin-18
Molecular weight formula_weight	19105.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1394

Structure of disulfide-stabilized IL-18 variant

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

Interleukin-18

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	121

fit	/app/data/saxs_computation/od/9od7/9od7.fit
pddf	/app/data/pr_computation/od/9od7/9od7.pr.out
profile	/app/data/saxs_computation/od/9od7/9od7.dat