7q50

human Gid4 bound to a Phe/N-peptide

Method: X-RAY DIFFRACTION D_max: 55.0 Å Quality: GOOD

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 121–290	Not recorded	FDVSWFMG peptide × 1	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

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 7Q50	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 oligomeric state 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 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 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 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 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 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 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 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 construct 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 construct 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 construct 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 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 oligomeric state 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 oligomeric state 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
7SLZ CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH BPF023596 Deposited 2021-10-25	Different construct 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 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 construct 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 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 construct 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 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 construct 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 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 construct 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 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 construct 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 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 construct 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 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 construct 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 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
7U3J GID4 in complex with compound 88 Deposited 2022-02-27	Different construct 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 124–289（166 aa）	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
7U3K GID4 in complex with compound 89 Deposited 2022-02-27	Different construct 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 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 construct 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 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 oligomeric state 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 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 construct 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 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 construct 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 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 construct 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 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 construct Different oligomeric state 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 construct Different oligomeric state 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 construct 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 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 construct 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 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 1–170； UniProt 121–290

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	7q50
Deposition date deposition_date	2021-11-02
Structure title title	human Gid4 bound to a Phe/N-peptide
Keywords keywords	GID, CTLH, ubiquitin, E3 ligase, 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	16.92 Å
Radius of gyration Rg (electron density) rg_electron	15.66 Å
Forward intensity I(0) i0	6754360.00
Molecular weight molecular_weight	19520.0 kDa
Excluded volume excluded_volume	24510 Å³
Envelope volume envelope_volume	27844 Å³
Hydration-shell volume shell_volume	14949 Å³
Envelope diameter envelope_diameter	54.9 Å
Shell Rg shell_rg	21.68 Å
Envelope Rg envelope_rg	16.00 Å
Shape Rg shape_rg	15.64 Å
Total Rg total_rg	16.78 Å
Total atoms total_atoms	1394
Residues n_residues	177
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	55.0 Å
Rg (real space) rg_real	16.83 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	6.7540e+06
I(0) uncertainty (real space) i0_real_error	7.0260e+04
Rg (reciprocal space) rg_reciprocal	16.85 Å
I(0) (reciprocal space) i0_reciprocal	6754000.0000
Solution quality estimate total_estimate	0.8761
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.3 Å
Skewness Skewness skewness	0.203
Kurtosis Kurtosis kurtosis	-0.274
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1610000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.933

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Glucose-induced degradation protein 4 homolog
Molecular weight formula_weight	20034.3 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	1403

LLYSGSKFRGHQKSKGNSYDVEVVLQHVDTGNSYLCGYLKIKGLTEEYPTLTTFFEGEIISKKHPFLTRKWDADEDVDRKHWGKFLAFYQYAKSFNSDDFDYEELKNGDYVFMRWKEQFLVPDHTIKDISGASFAGFYYICFQKSAASIEGYYYHRSSEWYQSLNLTHVP

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 polymer

Description description	FDVSWFMG peptide
Molecular weight formula_weight	931.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

FDVSWFM

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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8. Citations (1)

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Unit-cell length a length_a	131.307 Å
Unit-cell length b length_b	131.307 Å
Unit-cell length c length_c	131.307 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	24

Space group space_group	P 41 3 2
Space-group number int_tables_number	213
Crystal system crystal_system	—

Resolution resolution	3.160 Å
Low-resolution limit resolution_low	46.420 Å
R factor r_factor	0.2393
R_work r_work	0.2363
R_free r_free	0.2927

fit	/app/data/saxs_computation/q5/7q50/7q50.fit
pddf	/app/data/pr_computation/q5/7q50/7q50.pr.out
profile	/app/data/saxs_computation/q5/7q50/7q50.dat

human Gid4 bound to a Phe/N-peptide

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

Glucose-induced degradation protein 4 homolog

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)