3f62

Crystal Structure of Human IL-18 in complex with Ectromelia virus IL-18 Binding Protein

Method: X-RAY DIFFRACTION D_max: 69.5 Å Quality: GOOD

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

Interleukin 18 binding protein

Ectromelia virus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 21–126	Fragment：UNP residues 21-126	Interleukin-18 × 1 （Q14116）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q9IW12_9POXV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–109； UniProt 21–126

Interleukin-18

Homo sapiens

UniProt Q14116

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 37–193	Fragment：UNP residues 37-193 Mutation：C38S, C68S, C76S, C127S	Interleukin 18 binding protein × 1 （Q9IW12）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3F62	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 construct Different mutation/modification Different oligomeric state 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 construct 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
3WO2 Crystal structure of human interleukin-18 Deposited 2013-12-19	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 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 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 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 construct Different mutation/modification 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 construct Different mutation/modification 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 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 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification 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 mutation/modification Different oligomeric state 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
9OD7 Structure of disulfide-stabilized IL-18 variant Deposited 2025-04-25	Different construct Different mutation/modification Different oligomeric state 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；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
9OD9 Structure of disulfide-stabilized IL-18 variant Deposited 2025-04-25	Different construct Different mutation/modification Different oligomeric state 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–158； 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	3f62
Deposition date deposition_date	2008-11-05
Structure title title	Crystal Structure of Human IL-18 in complex with Ectromelia virus IL-18 Binding Protein
Keywords keywords	immunoglobulin, IL-18, beta trefoil, Cytokine, Secreted; 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	20.75 Å
Radius of gyration Rg (electron density) rg_electron	19.73 Å
Forward intensity I(0) i0	14688800.00
Molecular weight molecular_weight	28854.0 kDa
Excluded volume excluded_volume	36130 Å³
Envelope volume envelope_volume	43360 Å³
Hydration-shell volume shell_volume	18755 Å³
Envelope diameter envelope_diameter	69.9 Å
Shell Rg shell_rg	25.86 Å
Envelope Rg envelope_rg	20.23 Å
Shape Rg shape_rg	19.72 Å
Total Rg total_rg	20.65 Å
Total atoms total_atoms	2026
Residues n_residues	253
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	69.5 Å
Rg (real space) rg_real	20.74 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.4690e+07
I(0) uncertainty (real space) i0_real_error	1.8470e+05
Rg (reciprocal space) rg_reciprocal	20.74 Å
I(0) (reciprocal space) i0_reciprocal	14690000.0000
Solution quality estimate total_estimate	0.8074
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.346
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3802000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Interleukin 18 binding protein
Molecular weight formula_weight	12368.0 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	2146

GAMVETKCPNLDIVTSSGEFHCSGCVEHMPEFSYMYWLAKDMKSDEDTKFIEHLGDGINEDETVRTTDGGITTLRKVLHVTDTNKFAHYRFTCVLTTLDGVSKKNIWLK

来源 Source

来源生物 organism	Ectromelia virus
NCBI Class编号 ncbi_taxonomy_id	12643
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Interleukin-18
Molecular weight formula_weight	18232.5 kDa
Mutation mutation	C38S, C68S, C76S, C127S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GYFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDSRDNAPRTIFIISMYKDSQPRGMAVTISVKSEKISTLSSENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLASEKERDLFKLILKKEDELGDRSIMFTVQNED

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3f62b1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.1 — Cytokine
Family Family family	b.42.1.2 — Interleukin-1 (IL-1)

Domain ID domain_id	d3f62b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	3f62A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3f62B00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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8. Citations (1)

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Unit-cell length a length_a	36.356 Å
Unit-cell length b length_b	69.210 Å
Unit-cell length c length_c	104.832 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	34.610 Å
R factor r_factor	0.1909
R_work r_work	0.1886
R_free r_free	0.2354

fit	/app/data/saxs_computation/f6/3f62/3f62.fit
pddf	/app/data/pr_computation/f6/3f62/3f62.pr.out
profile	/app/data/saxs_computation/f6/3f62/3f62.dat

Crystal Structure of Human IL-18 in complex with Ectromelia virus IL-18 Binding Protein

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

Interleukin 18 binding protein

State in the Current Structure

Other States of the Same Protein in the Database

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)