13sa

PanDDA analysis group deposition -- IDOL RING domain in complex with Z1251361039

Method: X-RAY DIFFRACTION D_max: 65.9 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 369–445 Chain B； UniProt 369–445	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 369–445 Chain D； UniProt 369–445	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

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 13SA	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 ligand/ion 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 ligand/ion 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
13SB PanDDA analysis group deposition -- IDOL RING domain in complex with Z1456069604 Deposited 2025-10-10	Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 mutation/modification 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
6QLZ IDOL F3ab subdomain Deposited 2019-02-01	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 183–283（101 aa）	Not recorded	No recorded non-water small molecule	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
6QLZ IDOL F3ab subdomain Deposited 2019-02-01	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 183–283（101 aa）	Not recorded	No recorded non-water small molecule	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
6QLZ IDOL F3ab subdomain Deposited 2019-02-01	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 183–283（101 aa）	Not recorded	No recorded non-water small molecule	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
9SA1 The RING domain of IDOL Deposited 2025-08-07	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 ligand/ion 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 ligand/ion 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 69 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 2–78； UniProt 369–445 Author chain B； PDBConstruct 2–78； UniProt 369–445 Author chain C； PDBConstruct 2–78； UniProt 369–445 Author chain D； PDBConstruct 2–78； UniProt 369–445

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	13sa
Deposition date deposition_date	2025-10-10
最后修订 last_revision	2025-12-10
Structure title title	PanDDA analysis group deposition -- IDOL RING domain in complex with Z1251361039
Keywords keywords	Diamond I04-1 fragment screening, PanDDA, XChemExplorer, E3, ubiquitin, Zinc finger, RING, 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	21.30 Å
Radius of gyration Rg (electron density) rg_electron	20.38 Å
Forward intensity I(0) i0	40370900.00
Molecular weight molecular_weight	30643.0 kDa
Excluded volume excluded_volume	28385 Å³
Envelope volume envelope_volume	50713 Å³
Hydration-shell volume shell_volume	20802 Å³
Envelope diameter envelope_diameter	68.6 Å
Shell Rg shell_rg	26.79 Å
Envelope Rg envelope_rg	20.64 Å
Shape Rg shape_rg	20.43 Å
Total Rg total_rg	20.95 Å
Total atoms total_atoms	2227
Residues n_residues	282
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	65.9 Å
Rg (real space) rg_real	21.18 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	4.0370e+07
I(0) uncertainty (real space) i0_real_error	5.2050e+05
Rg (reciprocal space) rg_reciprocal	21.21 Å
I(0) (reciprocal space) i0_reciprocal	40370000.0000
Solution quality estimate total_estimate	0.8302
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.141
Kurtosis Kurtosis kurtosis	-0.460
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3095000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase MYLIP
Molecular weight formula_weight	8820.4 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2606

SQQTRVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTSLLNLTVI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(2R)-2-hydroxy-N-[(Z)-(pyridin-2-yl)methylidene]propanamide
Molecular weight formula_weight	178.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

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8. Citations (1)

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Unit-cell length a length_a	44.718 Å
Unit-cell length b length_b	48.054 Å
Unit-cell length c length_c	70.644 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.569 Å
Low-resolution limit resolution_low	70.640 Å
R factor r_factor	0.2015
R_work r_work	0.1999
R_free r_free	0.2341

fit	/app/data/saxs_computation/3s/13sa/13sa.fit
pddf	/app/data/pr_computation/3s/13sa/13sa.pr.out
profile	/app/data/saxs_computation/3s/13sa/13sa.dat