7u3j

GID4 in complex with compound 88

Method: X-RAY DIFFRACTION D_max: 54.7 Å Quality: REASONABLE

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

Glucose-induced degradation protein 4 homolog

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 124–289	Not recorded	GOL GLYCEROL × 2 L6U (2S)-2-{[(2S)-2-({N-[(2,4-dimethoxyphenyl)methyl]glycyl}amino)-2-(thiophen-2-yl)acetyl]amino}-N-methyl-4-phenylbutanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；18% PEG6000, 0.1 M HEPES	Resolution 1.64 Å R-free 0.202

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 7U3J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6CCR Selenomethionyl derivative of a GID4 fragment Deposited 2018-02-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 116–300（185 aa） Fragment：residues 116-300	Non-standard monomer：Yes (specific site not provided by mmCIF)	UNX UNKNOWN LIGAND × 36	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10% 2-propanol, 20% PEG4K and 0.1M Na-HEPES	Resolution 1.60 Å R-free 0.187
6CCT Fragment of GID4 in complex with a short peptide Deposited 2018-02-07	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 124–289（166 aa） Fragment：residues 124-289	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 2% Tacsimate pH 7.0 and 0.1M HEPES pH 7.5	Resolution 2.40 Å R-free 0.260
6CCU Complex between a GID4 fragment and a short peptide Deposited 2018-02-07	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 116–300（185 aa）	Not recorded	UNX UNKNOWN LIGAND × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350 and 0.03M Citric acid	Resolution 1.75 Å R-free 0.236
6CD8 Complex of GID4 fragment with short peptide Deposited 2018-02-08	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 124–289（166 aa） Fragment：residues 124-289	Not recorded	UNX UNKNOWN LIGAND × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000 and 0.1M KSCN	Resolution 1.60 Å R-free 0.224
6CD8 Complex of GID4 fragment with short peptide Deposited 2018-02-08	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 B 124–289（166 aa） Fragment：residues 124-289	Not recorded	UNX UNKNOWN LIGAND × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000 and 0.1M KSCN	Resolution 1.60 Å R-free 0.224
6CD9 GID4 in complex with a peptide Deposited 2018-02-08	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 124–289（166 aa） Fragment：residues 124-289	Not recorded	UNX UNKNOWN LIGAND × 46	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；24% PEG3350, 2.8% Tacsimate pH 7.0 and 0.1M HEPES pH 7.5	Resolution 1.55 Å R-free 0.193
6CDC GID4 in complex with a tetrapeptide Deposited 2018-02-08	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 124–289（166 aa） Fragment：residues 124-289	Not recorded	UNX UNKNOWN LIGAND × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30%PEG3350, 0.2M NaCl and 0.1M Tris pH 8.5	Resolution 1.75 Å R-free 0.239
6CDG GID4 fragment in complex with a peptide Deposited 2018-02-08	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 124–289（166 aa） Fragment：residues 124-289	Not recorded	UNX UNKNOWN LIGAND × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2M sodium bromide	Resolution 1.60 Å R-free 0.248
6WZX GID4 in complex with IGLWKS peptide Deposited 2020-05-14	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 124–289（166 aa）	Not recorded	UNX UNKNOWN LIGAND × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；20% (w/v) PEG 3350 and 8% (v/v) Tacsimate pH 7.0	Resolution 1.75 Å R-free 0.227
6WZX GID4 in complex with IGLWKS peptide Deposited 2020-05-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 124–289（166 aa）	Not recorded	UNX UNKNOWN LIGAND × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；20% (w/v) PEG 3350 and 8% (v/v) Tacsimate pH 7.0	Resolution 1.75 Å R-free 0.227
6WZZ GID4 in complex with VGLWKS peptide Deposited 2020-05-14	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 124–289（166 aa）	Not recorded	UNX UNKNOWN LIGAND × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.03 M Citric acid, pH 7.6 and 20% (w/v) PEG 3350	Resolution 1.60 Å R-free 0.220
7NSC Substrate receptor scaffolding module of human CTLH E3 ubiquitin ligase Deposited 2021-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–300（300 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7Q4Y human Gid4 bound to a Gly/N-peptide Deposited 2021-11-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–300（201 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；18% PEG 3350, 0.2 M ammonium nitrate, 0.1 M Bis-Tris pH 7	Resolution 3.08 Å R-free 0.265
7Q4Y human Gid4 bound to a Gly/N-peptide Deposited 2021-11-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 100–300（201 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；18% PEG 3350, 0.2 M ammonium nitrate, 0.1 M Bis-Tris pH 7	Resolution 3.08 Å R-free 0.265
7Q50 human Gid4 bound to a Phe/N-peptide Deposited 2021-11-02	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 121–290（170 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.1 M Sodium malonate, 0.3% Jeffamine ED-2001 pH 7, 0.1 M HEPES pH 7	Resolution 3.16 Å R-free 0.293
7SLZ CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH BPF023596 Deposited 2021-10-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	9QU N-[(1s,4s)-4-(1H-benzimidazol-2-yl)cyclohexyl]-N~2~-[(1H-indol-2-yl)methyl]glycinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；35% PEG 3350, 0.2M CaAC	Resolution 1.97 Å R-free 0.246
7U3E GID4 in complex with compound 1 Deposited 2022-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	L4O tert-butyl (1S,4S)-2,5-diazabicyclo[2.2.1]heptane-2-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；17% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium acetate	Resolution 1.85 Å R-free 0.234
7U3E GID4 in complex with compound 1 Deposited 2022-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 124–289（166 aa）	Not recorded	L4O tert-butyl (1S,4S)-2,5-diazabicyclo[2.2.1]heptane-2-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；17% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium acetate	Resolution 1.85 Å R-free 0.234
7U3F GID4 in complex with compound 4 Deposited 2022-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	GOL GLYCEROL × 1 L5L (4R)-4-(4-methoxyphenyl)-4,5,6,7-tetrahydrothieno[3,2-c]pyridine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG5000 MME, 0.1 M Bis-tris	Resolution 2.30 Å R-free 0.262
7U3G GID4 in complex with compound 67 Deposited 2022-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	L6F (1R)-1-phenyl-1,2,3,4-tetrahydroisoquinolin-5-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium acetate	Resolution 2.24 Å R-free 0.240
7U3H GID4 in complex with compound 7 Deposited 2022-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	L6O (5R)-N-(4-fluorophenyl)-5-methyl-4,5-dihydro-1,3-thiazol-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium formate	Resolution 1.80 Å R-free 0.224
7U3I GID4 in complex with compound 16 Deposited 2022-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	L5X 3-{[(5S)-5-methyl-4,5-dihydro-1,3-thiazol-2-yl]amino}phenol × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；16% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium formate	Resolution 1.99 Å R-free 0.230
7U3I GID4 in complex with compound 16 Deposited 2022-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 124–289（166 aa）	Not recorded	L5X 3-{[(5S)-5-methyl-4,5-dihydro-1,3-thiazol-2-yl]amino}phenol × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；16% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium formate	Resolution 1.99 Å R-free 0.230
7U3K GID4 in complex with compound 89 Deposited 2022-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	L73 N-butylglycyl-4-tert-butyl-D-phenylalanyl-3-methoxy-N-methyl-L-phenylalaninamide × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% PEG6000, 0.1 M HEPES, 0.2 M calcium chloride	Resolution 2.20 Å R-free 0.313
7U3L GID4 in complex with compound 91 Deposited 2022-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	L4X Nalpha-{(2R,4E)-2-[(N-benzylglycyl)amino]-5-phenylpent-4-enoyl}-N,4-dimethyl-L-phenylalaninamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG3350, 0.2 M sodium fluoride	Resolution 2.29 Å R-free 0.249
8V1P CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH UBF9092 Deposited 2023-11-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa） Fragment：Residues 124-289	Not recorded	98C N,N~2~-bis[(4-methoxyphenyl)methyl]glycinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M Tris-HCl 8.5, 30% PEG3350, 0.2 M MgCl2	Resolution 2.21 Å R-free 0.278
8X7G Crystal structure of the ternary complex of GID4-PROTAC(NEP108)-BRD4(BD1). Deposited 2023-11-24	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 124–289（166 aa）	Not recorded	YAX 2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]-~{N}-[2-[2-[[2-[4-[2-(1~{H}-indol-2-ylmethylamino)ethanoylamino]cyclohexyl]-3~{H}-benzimidazol-5-yl]oxy]ethoxy]ethyl]ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Bis-Tris pH 6.5, 25% (v/v) polyethylene glycol 300, 30% (v/v) galactose	Resolution 2.70 Å R-free 0.266
8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24	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 124–289（166 aa）	Not recorded	YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000	Resolution 2.90 Å R-free 0.301
8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24	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 124–289（166 aa）	Not recorded	YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000	Resolution 2.90 Å R-free 0.301
8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24	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 124–289（166 aa）	Not recorded	YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000	Resolution 2.90 Å R-free 0.301
8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24	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 124–289（166 aa）	Not recorded	YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000	Resolution 2.90 Å R-free 0.301
9OK4 GID4 in complex with CLEO4-88 and ACAA1 Deposited 2025-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 124–289（166 aa） Chain D 124–289（166 aa）	Not recorded	L6U (2S)-2-{[(2S)-2-({N-[(2,4-dimethoxyphenyl)methyl]glycyl}amino)-2-(thiophen-2-yl)acetyl]amino}-N-methyl-4-phenylbutanamide × 2 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.1 M Tris pH 7.5 and 0.2 M NaF	Resolution 2.28 Å R-free 0.230
9QDX GID4 in complex with Compound 1 Deposited 2025-03-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	A1I6C ~{N}'-phenylpiperidine-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350	Resolution 2.26 Å R-free 0.296
9QDY GID4 in complex with Compound 9 Deposited 2025-03-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	A1I6B ~{N}-[3-fluoranyl-5-(5-methylfuran-2-yl)phenyl]-4-methyl-piperidine-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Na HEPES pH 7.0, 15% PEG 3350	Resolution 2.10 Å R-free 0.254
9QDZ GID4 in complex with Compound 14 Deposited 2025-03-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	A1I6F ~{N}-[3-fluoranyl-5-(5-methyl-4-piperidin-1-ylcarbonyl-furan-2-yl)phenyl]-4,4-dimethyl-piperidine-1-carboximidamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；0.1 M Na HEPES 7.5, 7.5% 2-propanol, 20% PEG 4000	Resolution 1.80 Å R-free 0.244
9QZG GID4 in complex with Compound 18 Deposited 2025-04-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	A1JCC ~{N}-[3-fluoranyl-5-[4-(4-methoxypiperidin-1-yl)carbonyl-5-methyl-furan-2-yl]phenyl]-4,4-dimethyl-piperidine-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 22.5% PEG 4000	Resolution 1.90 Å R-free 0.336
9QZH GID4 in complex with Compound 33 Deposited 2025-04-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 20% PEG 4000	Resolution 2.19 Å R-free 0.220
9QZH GID4 in complex with Compound 33 Deposited 2025-04-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 124–289（166 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 20% PEG 4000	Resolution 2.19 Å R-free 0.220
9QZH GID4 in complex with Compound 33 Deposited 2025-04-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 124–289（166 aa）	Not recorded	A1JCD ~{N}-[3-fluoranyl-5-[4-[4-(methoxymethyl)piperidin-1-yl]carbonyl-5-methyl-furan-2-yl]phenyl]-4,4-dimethyl-piperidine-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 20% PEG 4000	Resolution 2.19 Å R-free 0.220
9QZH GID4 in complex with Compound 33 Deposited 2025-04-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 124–289（166 aa）	Not recorded	A1JCD ~{N}-[3-fluoranyl-5-[4-[4-(methoxymethyl)piperidin-1-yl]carbonyl-5-methyl-furan-2-yl]phenyl]-4,4-dimethyl-piperidine-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 20% PEG 4000	Resolution 2.19 Å R-free 0.220
9QZI GID4 in complex with Compound 21 Deposited 2025-04-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 124–289（166 aa）	Not recorded	A1JCE ~{N}-[3-fluoranyl-5-[4-[(3~{S})-3-[2-(2-methoxyethoxy)ethyl]piperidin-1-yl]carbonyl-5-methyl-furan-2-yl]phenyl]-4,4-dimethyl-piperidine-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Na HEPES pH 7.5,0.1 M lithium sulfate, 22.5% PEG 4000	Resolution 2.00 Å R-free 0.253

30 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GID4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–167； UniProt 124–289

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	7u3j
Deposition date deposition_date	2022-02-27
Structure title title	GID4 in complex with compound 88
Keywords keywords	Complex, Inhibitor, Protein degradation, PEPTIDE BINDING PROTEIN, PEPTIDE BINDING PROTEIN-INHIBITOR complex; PEPTIDE BINDING PROTEIN/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.78 Å
Radius of gyration Rg (electron density) rg_electron	15.52 Å
Forward intensity I(0) i0	6739670.00
Molecular weight molecular_weight	19567.0 kDa
Excluded volume excluded_volume	24651 Å³
Envelope volume envelope_volume	27394 Å³
Hydration-shell volume shell_volume	14797 Å³
Envelope diameter envelope_diameter	55.7 Å
Shell Rg shell_rg	21.51 Å
Envelope Rg envelope_rg	15.86 Å
Shape Rg shape_rg	15.49 Å
Total Rg total_rg	16.71 Å
Total atoms total_atoms	2621
Residues n_residues	166
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	54.7 Å
Rg (real space) rg_real	16.69 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	6.7400e+06
I(0) uncertainty (real space) i0_real_error	6.9680e+04
Rg (reciprocal space) rg_reciprocal	16.70 Å
I(0) (reciprocal space) i0_reciprocal	6740000.0000
Solution quality estimate total_estimate	0.6498
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.213
Kurtosis Kurtosis kurtosis	-0.266
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	1665000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.995; 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)

Entity 1 Entity 1 polymer

Description description	Glucose-induced degradation protein 4 homolog
Molecular weight formula_weight	19604.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2733

GSGSKFRGHQKSKGNSYDVEVVLQHVDTGNSYLCGYLKIKGLTEEYPTLTTFFEGEIISKKHPFLTRKWDADEDVDRKHWGKFLAFYQYAKSFNSDDFDYEELKNGDYVFMRWKEQFLVPDHTIKDISGASFAGFYYICFQKSAASIEGYYYHRSSEWYQSLNLTHV

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	(2S)-2-{[(2S)-2-({N-[(2,4-dimethoxyphenyl)methyl]glycyl}amino)-2-(thiophen-2-yl)acetyl]amino}-N-methyl-4-phenylbutanamide
Molecular weight formula_weight	538.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	112

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8. Citations (1)

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Unit-cell length a length_a	40.350 Å
Unit-cell length b length_b	58.530 Å
Unit-cell length c length_c	69.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.642 Å
Low-resolution limit resolution_low	44.662 Å
R factor r_factor	0.1841
R_work r_work	0.1831
R_free r_free	0.2023

fit	/app/data/saxs_computation/u3/7u3j/7u3j.fit
pddf	/app/data/pr_computation/u3/7u3j/7u3j.pr.out
profile	/app/data/saxs_computation/u3/7u3j/7u3j.dat