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13sx

PanDDA analysis group deposition -- IDOL RING domain in complex with POB0134

Method: X-RAY DIFFRACTION Dmax: 66.4 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase MYLIP

Homo sapiens

UniProt Q8WY64

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 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
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 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

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 13SX 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
13SA PanDDA analysis group deposition -- IDOL RING domain in complex with Z1251361039 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
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 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 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

SAXS profile for 13sx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 13sx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id13sx
Deposition date deposition_date2025-10-10
最后修订 last_revision2025-12-10
Structure title titlePanDDA analysis group deposition -- IDOL RING domain in complex with POB0134
Keywords keywordsDiamond I04-1 fragment screening, PanDDA, XChemExplorer, E3, ubiquitin, Zinc finger, RING, ligase; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.41 Å
Radius of gyration Rg (electron density) rg_electron20.51 Å
Forward intensity I(0) i038733000.00
Molecular weight molecular_weight30045.0 kDa
Excluded volume excluded_volume27855 ų
Envelope volume envelope_volume50234 ų
Hydration-shell volume shell_volume20496 ų
Envelope diameter envelope_diameter68.7 Å
Shell Rg shell_rg26.87 Å
Envelope Rg envelope_rg20.67 Å
Shape Rg shape_rg20.57 Å
Total Rg total_rg21.06 Å
Total atoms total_atoms2185
Residues n_residues277
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax66.4 Å
Rg (real space) rg_real21.29 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real3.8730e+07
I(0) uncertainty (real space) i0_real_error4.8870e+05
Rg (reciprocal space) rg_reciprocal21.31 Å
I(0) (reciprocal space) i0_reciprocal38730000.0000
Solution quality estimate total_estimate0.9094
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3 Å
Skewness Skewness skewness0.119
Kurtosis Kurtosis kurtosis-0.492
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2504000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)