6qlz

IDOL F3ab subdomain

Method: X-RAY DIFFRACTION D_max: 86.0 Å Quality: GOOD

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

E3 ubiquitin-protein ligase MYLIP

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 183–283	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100mM Hepes pH 7.0 10% (w/v) PEG 6000	Resolution 2.34 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 183–283	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100mM Hepes pH 7.0 10% (w/v) PEG 6000	Resolution 2.34 Å
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 183–283	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100mM Hepes pH 7.0 10% (w/v) PEG 6000	Resolution 2.34 Å

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 6QLZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
13RZ PanDDA analysis group deposition -- IDOL RING domain in complex with Z1118527729 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1CX8 2-{[(1R,2R)-2-methylcyclopentyl]amino}ethan-1-ol × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.66 Å R-free 0.229
13RZ PanDDA analysis group deposition -- IDOL RING domain in complex with Z1118527729 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1CX8 2-{[(1R,2R)-2-methylcyclopentyl]amino}ethan-1-ol × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.66 Å R-free 0.229
13SA PanDDA analysis group deposition -- IDOL RING domain in complex with Z1251361039 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 ACT ACETATE ION × 1 A1CYA (2R)-2-hydroxy-N-[(Z)-(pyridin-2-yl)methylidene]propanamide × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.57 Å R-free 0.234
13SA PanDDA analysis group deposition -- IDOL RING domain in complex with Z1251361039 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.57 Å R-free 0.234
13SB PanDDA analysis group deposition -- IDOL RING domain in complex with Z1456069604 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 KF8 N-[(3S)-piperidin-3-yl]benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.48 Å R-free 0.218
13SB PanDDA analysis group deposition -- IDOL RING domain in complex with Z1456069604 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 KF8 N-[(3S)-piperidin-3-yl]benzamide × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.48 Å R-free 0.218
13SC PanDDA analysis group deposition -- IDOL RING domain in complex with Z1491353358 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 WNM (3S)-1-(phenylsulfonyl)pyrrolidin-3-amine × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.48 Å R-free 0.209
13SC PanDDA analysis group deposition -- IDOL RING domain in complex with Z1491353358 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 WNM (3S)-1-(phenylsulfonyl)pyrrolidin-3-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.48 Å R-free 0.209
13SD PanDDA analysis group deposition -- IDOL RING domain in complex with Z1516316257 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1CYB 3-ethyl-5-methyl-4-[(3-methyl-1H-pyrazol-1-yl)methyl]-1,2-oxazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.52 Å R-free 0.192
13SD PanDDA analysis group deposition -- IDOL RING domain in complex with Z1516316257 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.52 Å R-free 0.192
13SE PanDDA analysis group deposition -- IDOL RING domain in complex with Z1587220559 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.44 Å R-free 0.198
13SE PanDDA analysis group deposition -- IDOL RING domain in complex with Z1587220559 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 T1J 2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.44 Å R-free 0.198
13SF PanDDA analysis group deposition -- IDOL RING domain in complex with Z1685106505 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 TQC (3M)-5-cyclobutyl-3-(1-methyl-1H-imidazol-2-yl)-1,2,4-oxadiazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.71 Å R-free 0.265
13SF PanDDA analysis group deposition -- IDOL RING domain in complex with Z1685106505 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.71 Å R-free 0.265
13SG PanDDA analysis group deposition -- IDOL RING domain in complex with Z1891773476 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 DMS DIMETHYL SULFOXIDE × 1 A1BNE 1-[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]-N-methylmethanamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.73 Å R-free 0.239
13SG PanDDA analysis group deposition -- IDOL RING domain in complex with Z1891773476 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 DMS DIMETHYL SULFOXIDE × 1 A1BNE 1-[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]-N-methylmethanamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.73 Å R-free 0.239
13SH PanDDA analysis group deposition -- IDOL RING domain in complex with Z234898049 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1CYF 3-(5-methyl-1,2,4-oxadiazol-3-yl)aniline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.60 Å R-free 0.233
13SH PanDDA analysis group deposition -- IDOL RING domain in complex with Z234898049 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1CYF 3-(5-methyl-1,2,4-oxadiazol-3-yl)aniline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.60 Å R-free 0.233
13SI PanDDA analysis group deposition -- IDOL RING domain in complex with Z2574937229 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 WJG (S)-1-(4-methoxyphenyl)-1-phenylmethanamine × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.54 Å R-free 0.211
13SI PanDDA analysis group deposition -- IDOL RING domain in complex with Z2574937229 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 WJG (S)-1-(4-methoxyphenyl)-1-phenylmethanamine × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.54 Å R-free 0.211
13SJ PanDDA analysis group deposition -- IDOL RING domain in complex with Z2643472210 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 JGY 1-methyl-N-{[(2S)-oxolan-2-yl]methyl}-1H-pyrazole-3-carboxamide × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.47 Å R-free 0.204
13SJ PanDDA analysis group deposition -- IDOL RING domain in complex with Z2643472210 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.47 Å R-free 0.204
13SK PanDDA analysis group deposition -- IDOL RING domain in complex with Z2692078340 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 W1Y N-methyl-1-(1-phenyl-1H-pyrazol-4-yl)methanamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.54 Å R-free 0.230
13SK PanDDA analysis group deposition -- IDOL RING domain in complex with Z2692078340 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 W1Y N-methyl-1-(1-phenyl-1H-pyrazol-4-yl)methanamine × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.54 Å R-free 0.230
13SL PanDDA analysis group deposition -- IDOL RING domain in complex with Z275151340 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 JHP 4-chloro-N-cyclopentyl-1-methyl-1H-pyrazole-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.34 Å R-free 0.214
13SL PanDDA analysis group deposition -- IDOL RING domain in complex with Z275151340 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 JHP 4-chloro-N-cyclopentyl-1-methyl-1H-pyrazole-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.34 Å R-free 0.214
13SM PanDDA analysis group deposition -- IDOL RING domain in complex with Z275179946 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 GW1 (4-chloranyl-2-methyl-pyrazol-3-yl)-piperidin-1-yl-methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.40 Å R-free 0.205
13SM PanDDA analysis group deposition -- IDOL RING domain in complex with Z275179946 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 GW1 (4-chloranyl-2-methyl-pyrazol-3-yl)-piperidin-1-yl-methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.40 Å R-free 0.205
13SN PanDDA analysis group deposition -- IDOL RING domain in complex with Z2757439080 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 Q7L (3P)-3-(2H-1,3-benzodioxol-5-yl)-1H-pyrazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.44 Å R-free 0.204
13SN PanDDA analysis group deposition -- IDOL RING domain in complex with Z2757439080 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 Q7L (3P)-3-(2H-1,3-benzodioxol-5-yl)-1H-pyrazole × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.44 Å R-free 0.204
13SO PanDDA analysis group deposition -- IDOL RING domain in complex with Z285233820 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 KB3 (5M)-5-(2-methoxyphenyl)-1,3,4-oxadiazol-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.61 Å R-free 0.226
13SO PanDDA analysis group deposition -- IDOL RING domain in complex with Z285233820 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 KB3 (5M)-5-(2-methoxyphenyl)-1,3,4-oxadiazol-2-amine × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.61 Å R-free 0.226
13SP PanDDA analysis group deposition -- IDOL RING domain in complex with Z364577298 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1CYC 1-[(3S)-3-methylmorpholin-4-yl]-2-[3-(trifluoromethyl)-1H-pyrazol-1-yl]ethan-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.69 Å R-free 0.261
13SP PanDDA analysis group deposition -- IDOL RING domain in complex with Z364577298 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.69 Å R-free 0.261
13SQ PanDDA analysis group deposition -- IDOL RING domain in complex with Z369936976 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 U0P N'-cyclopropyl-N-methyl-N-[(5-methyl-1,2-oxazol-3-yl)methyl]urea × 1 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.30 Å R-free 0.200
13SQ PanDDA analysis group deposition -- IDOL RING domain in complex with Z369936976 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 U0P N'-cyclopropyl-N-methyl-N-[(5-methyl-1,2-oxazol-3-yl)methyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.30 Å R-free 0.200
13SR PanDDA analysis group deposition -- IDOL RING domain in complex with Z48852953 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1CYD 4-methyl-N-{[(2S)-oxolan-2-yl]methyl}-1,3-thiazol-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.65 Å R-free 0.230
13SR PanDDA analysis group deposition -- IDOL RING domain in complex with Z48852953 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1CYD 4-methyl-N-{[(2S)-oxolan-2-yl]methyl}-1,3-thiazol-2-amine × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.65 Å R-free 0.230
13SS PanDDA analysis group deposition -- IDOL RING domain in complex with Z57475877 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 S7S ~{N}-(2-ethyl-1,2,3,4-tetrazol-5-yl)butanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.69 Å R-free 0.234
13SS PanDDA analysis group deposition -- IDOL RING domain in complex with Z57475877 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.69 Å R-free 0.234
13ST PanDDA analysis group deposition -- IDOL RING domain in complex with Z608065044 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.37 Å R-free 0.200
13ST PanDDA analysis group deposition -- IDOL RING domain in complex with Z608065044 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1H9V ~{N},~{N}-dimethyl-1~{H}-pyrazole-4-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.37 Å R-free 0.200
13SU PanDDA analysis group deposition -- IDOL RING domain in complex with Z68404778 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 B1A ~{N}-(4-phenylazanylphenyl)ethanamide × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.50 Å R-free 0.201
13SU PanDDA analysis group deposition -- IDOL RING domain in complex with Z68404778 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.50 Å R-free 0.201
13SV PanDDA analysis group deposition -- IDOL RING domain in complex with Z954606858 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 VW4 (2S)-2-phenylpropane-1-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.68 Å R-free 0.233
13SV PanDDA analysis group deposition -- IDOL RING domain in complex with Z954606858 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.68 Å R-free 0.233
13SW PanDDA analysis group deposition -- IDOL RING domain in complex with POB0087 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1AJM (3S)-3-(4-fluorophenyl)piperidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.37 Å R-free 0.213
13SW PanDDA analysis group deposition -- IDOL RING domain in complex with POB0087 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.37 Å R-free 0.213
13SX PanDDA analysis group deposition -- IDOL RING domain in complex with POB0134 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.36 Å R-free 0.199
13SX PanDDA analysis group deposition -- IDOL RING domain in complex with POB0134 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1CYE methyl (3R,4R)-4-(3-methoxyphenyl)oxane-3-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.36 Å R-free 0.199
13SY PanDDA analysis group deposition -- IDOL RING domain in complex with POB0041 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 W2J [(3R,5R)-5-methylpiperidin-3-yl]methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.29 Å R-free 0.203
13SY PanDDA analysis group deposition -- IDOL RING domain in complex with POB0041 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 W2J [(3R,5R)-5-methylpiperidin-3-yl]methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.29 Å R-free 0.203
13SZ PanDDA analysis group deposition -- IDOL RING domain in complex with NCL-00023835 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1H6Y 1-bromanyl-4-methylsulfonyl-benzene × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.49 Å R-free 0.214
13SZ PanDDA analysis group deposition -- IDOL RING domain in complex with NCL-00023835 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 A1H6Y 1-bromanyl-4-methylsulfonyl-benzene × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.49 Å R-free 0.214
13TA PanDDA analysis group deposition -- IDOL RING domain in complex with Z1741976468 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 XJV imidazolidin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.51 Å R-free 0.222
13TA PanDDA analysis group deposition -- IDOL RING domain in complex with Z1741976468 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 XJV imidazolidin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.51 Å R-free 0.222
13TB PanDDA analysis group deposition -- IDOL RING domain in complex with Z2301685688 Deposited 2025-10-10	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 W3M 1H-imidazole-5-carbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.55 Å R-free 0.218
13TB PanDDA analysis group deposition -- IDOL RING domain in complex with Z2301685688 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 W3M 1H-imidazole-5-carbonitrile × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.55 Å R-free 0.218
2YHN The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04	Different construct Different mutation/modification 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 369–445（77 aa） Fragment：RING, RESIDUES 369-445 Chain B 369–445（77 aa） Fragment：RING, RESIDUES 369-445	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M SODIUM ACETATE PH 7-8, 16-20% MPD.	Resolution 3.00 Å R-free 0.297
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 369–445（77 aa） Fragment：RING, RESIDUES 369-445	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000	Resolution 2.10 Å R-free 0.233
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Fragment：RING, RESIDUES 369-445	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000	Resolution 2.10 Å R-free 0.233
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 369–445（77 aa） Fragment：RING, RESIDUES 369-445	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000	Resolution 2.10 Å R-free 0.233
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 369–445（77 aa） Fragment：RING, RESIDUES 369-445	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000	Resolution 2.10 Å R-free 0.233
6QLY IDOL FERM domain Deposited 2019-02-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–344（344 aa）	Not recorded	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100mM Tris pH 8.5, 20mM MgSO4, 4% (w/v) ethylene glycol, 12% (w/v) 2-Methyl-2,4-pentanediol (MPD)	Resolution 2.50 Å R-free 0.247
6QLY IDOL FERM domain Deposited 2019-02-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–344（344 aa）	Not recorded	SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100mM Tris pH 8.5, 20mM MgSO4, 4% (w/v) ethylene glycol, 12% (w/v) 2-Methyl-2,4-pentanediol (MPD)	Resolution 2.50 Å R-free 0.247
9SA1 The RING domain of IDOL Deposited 2025-08-07	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；200 mM Magnesium chloride hexahydrate, 100 mM Bis-tris, 25% w/v PEG 3350	Resolution 1.06 Å R-free 0.177
9SA2 The RING domain of IDOL Deposited 2025-08-07	Different construct Different mutation/modification 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 369–445（77 aa） Chain B 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.10 Å R-free 0.174
9SA2 The RING domain of IDOL Deposited 2025-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 369–445（77 aa） Chain D 369–445（77 aa）	Not recorded	ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000	Resolution 1.10 Å R-free 0.174

34 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MYLIP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–101； UniProt 183–283 Author chain B； PDBConstruct 1–101； UniProt 183–283 Author chain C； PDBConstruct 1–101； UniProt 183–283

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	6qlz
Deposition date deposition_date	2019-02-01
Structure title title	IDOL F3ab subdomain
Keywords keywords	E3 LIGASE CHOLESTEROL METABOLISM LDLR degradation, LIGASE; LIGASE
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	23.77 Å
Radius of gyration Rg (electron density) rg_electron	22.93 Å
Forward intensity I(0) i0	17003300.00
Molecular weight molecular_weight	31319.0 kDa
Excluded volume excluded_volume	39401 Å³
Envelope volume envelope_volume	52065 Å³
Hydration-shell volume shell_volume	19980 Å³
Envelope diameter envelope_diameter	89.7 Å
Shell Rg shell_rg	28.33 Å
Envelope Rg envelope_rg	23.11 Å
Shape Rg shape_rg	22.91 Å
Total Rg total_rg	23.75 Å
Total atoms total_atoms	2202
Residues n_residues	285
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	86.0 Å
Rg (real space) rg_real	23.81 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	1.7000e+07
I(0) uncertainty (real space) i0_real_error	2.6920e+05
Rg (reciprocal space) rg_reciprocal	23.80 Å
I(0) (reciprocal space) i0_reciprocal	17000000.0000
Solution quality estimate total_estimate	0.7616
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.353
Kurtosis Kurtosis kurtosis	-0.338
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3230000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.696; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.813; 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	56.365 Å
Unit-cell length b length_b	69.536 Å
Unit-cell length c length_c	74.318 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	12

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

Resolution resolution	2.343 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Description description	E3 ubiquitin-protein ligase MYLIP
Molecular weight formula_weight	11129.6 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2213

IDOL F3ab subdomain

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

E3 ubiquitin-protein ligase MYLIP

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	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

fit	/app/data/saxs_computation/ql/6qlz/6qlz.fit
pddf	/app/data/pr_computation/ql/6qlz/6qlz.pr.out
profile	/app/data/saxs_computation/ql/6qlz/6qlz.dat