SAXSdb — 5lxi

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

Gamma-aminobutyric acid receptor-associated protein-like 1

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–117 Chain D； UniProt 1–117	Not recorded	Cysteine protease ATG4B × 2 （Q9Y4P1） MG MAGNESIUM ION × 3 PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 1 PER PEROXIDE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MgCl2, 24.6 % PEG 400, 29.5 % PEG 8000, 0.1M TRIS 8.5	Resolution 1.44 Å R-free 0.230

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 5LXI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L8J GABARAPL-1 NBR1-LIR complex structure Deposited 2011-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.6 mM [U-98% 15N] GABARAPL-1, 0.9 mM NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6 mM [U-98% 13C; U-98% 15N] GABARAPL-1, 0.9 mM NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.9 mM GABARAPL-1, 0.6 mM [U-98% 15N] NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.9 mM GABARAPL-1, 0.6 mM [U-98% 13C; U-98% 15N] NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2R2Q Crystal structure of human Gamma-Aminobutyric Acid Receptor-Associated Protein-like 1 (GABARAP1), Isoform CRA_a Deposited 2007-08-27	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 3–111（109 aa）	Not recorded	UNX UNKNOWN LIGAND × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG 3350, 0.2M Sodium chloride, 0.1M Hepes, 5% MPD, pH 7.5, VAPOR DIFFUSION, temperature 291K	Resolution 1.65 Å R-free 0.234
2R2Q Crystal structure of human Gamma-Aminobutyric Acid Receptor-Associated Protein-like 1 (GABARAP1), Isoform CRA_a Deposited 2007-08-27	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 3–111（109 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG 3350, 0.2M Sodium chloride, 0.1M Hepes, 5% MPD, pH 7.5, VAPOR DIFFUSION, temperature 291K	Resolution 1.65 Å R-free 0.234
5DPT Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117 Deposited 2015-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–117（116 aa） Fragment：UNP Q9Y4G2 627-638, UNP Q9H0R8 2-117	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；278 K；20% w/v Polyethylene glycol 3,350, 0.2 M NaCl, 8% MPD pH 7.2	Resolution 2.90 Å R-free 0.260
5DPT Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117 Deposited 2015-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–117（116 aa） Fragment：UNP Q9Y4G2 627-638, UNP Q9H0R8 2-117	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；278 K；20% w/v Polyethylene glycol 3,350, 0.2 M NaCl, 8% MPD pH 7.2	Resolution 2.90 Å R-free 0.260
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21	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 1–117（117 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol	Resolution 1.58 Å R-free 0.237
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21	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 B 1–117（117 aa）	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol	Resolution 1.58 Å R-free 0.237
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21	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 C 1–117（117 aa）	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol	Resolution 1.58 Å R-free 0.237
6HOI Structure of Beclin1 LIR motif bound to GABARAPL1 Deposited 2018-09-17	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 1–117（117 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium acetate, 0.1M Hepes pH 7.5, 12% PEG 4000	Resolution 1.14 Å R-free 0.166
6HOI Structure of Beclin1 LIR motif bound to GABARAPL1 Deposited 2018-09-17	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 B 1–117（117 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium acetate, 0.1M Hepes pH 7.5, 12% PEG 4000	Resolution 1.14 Å R-free 0.166
6HOL Structure of ATG14 LIR motif bound to GABARAPL1 Deposited 2018-09-17	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 1–117（117 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；289 K；1M LiCl, 0.1M HEPES pH7, 20% PEG 6000	Resolution 1.40 Å R-free 0.203
6HOL Structure of ATG14 LIR motif bound to GABARAPL1 Deposited 2018-09-17	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 B 1–117（117 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；289 K；1M LiCl, 0.1M HEPES pH7, 20% PEG 6000	Resolution 1.40 Å R-free 0.203
6YOO Structure of SAMM50 LIR bound to GABARAPL1 Deposited 2020-04-14	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 1–117（117 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；24% w/v PEG 6000, 10 mM ZnCl2 and 0.1 M Tris pH 7.5	Resolution 1.06 Å R-free 0.147
7AA7 Structure of SCOC pS12/pS18 LIR motif bound to GABARAPL1 Deposited 2020-09-03	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 1–117（117 aa）	Not recorded	SAT sulfoacetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M MES pH 6.5, 3.5M AMSO4, 1% MPD	Resolution 1.45 Å R-free 0.189
7AA7 Structure of SCOC pS12/pS18 LIR motif bound to GABARAPL1 Deposited 2020-09-03	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 B 1–117（117 aa）	Not recorded	SAT sulfoacetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M MES pH 6.5, 3.5M AMSO4, 1% MPD	Resolution 1.45 Å R-free 0.189
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03	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 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8	Resolution 1.72 Å R-free 0.261
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03	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 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8	Resolution 1.72 Å R-free 0.261
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03	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 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8	Resolution 1.72 Å R-free 0.261
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03	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 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8	Resolution 1.72 Å R-free 0.261
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8	Resolution 1.72 Å R-free 0.261
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8	Resolution 1.72 Å R-free 0.261
7JHX Crystal structure of hEPG5 LIR/GABARAPL1 complex Deposited 2020-07-21	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 1–117（117 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M ammonium sulfate, 0.1 MES buffer pH 5.5, 29% (w/v) PEG 4000	Resolution 1.91 Å R-free 0.245
7JHX Crystal structure of hEPG5 LIR/GABARAPL1 complex Deposited 2020-07-21	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 B 1–117（117 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M ammonium sulfate, 0.1 MES buffer pH 5.5, 29% (w/v) PEG 4000	Resolution 1.91 Å R-free 0.245
8X8A Crystal structure of STBD1 LIR motif in complex with GABARAPL1 Deposited 2023-11-27	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 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；25% w/v Pentaerythritol Propoxylate (5/4 PO/OH), 0.1 M Sodium acetate pH 4.6, 0.05 M Magnesium chloride	Resolution 1.53 Å R-free 0.187
9HGC Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8 Deposited 2024-11-19	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 1–117（117 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol	Resolution 2.52 Å R-free 0.259
9HGC Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8 Deposited 2024-11-19	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 1–117（117 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol	Resolution 2.52 Å R-free 0.259
9HGC Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8 Deposited 2024-11-19	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 1–117（117 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol	Resolution 2.52 Å R-free 0.259
9HGC Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8 Deposited 2024-11-19	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 1–117（117 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol	Resolution 2.52 Å R-free 0.259
9JF2 Crystal structure of GABARAPL1 in complex with ATG16L1 Deposited 2024-09-03	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 1–117（117 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000	Resolution 1.76 Å R-free 0.215
9JF2 Crystal structure of GABARAPL1 in complex with ATG16L1 Deposited 2024-09-03	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 B 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000	Resolution 1.76 Å R-free 0.215

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

View Construct and Data Evidence

UniProt name	GBRL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 7–123； UniProt 1–117 Author chain D； PDBConstruct 7–123； UniProt 1–117

Cysteine protease ATG4B

OrganismNot specified

UniProt Q9Y4P1

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 384–393 Chain E； UniProt 384–393	Fragment：UNP residues 384-393 Non-standard monomer：Yes (specific site not provided by mmCIF)	Gamma-aminobutyric acid receptor-associated protein-like 1 × 2 （Q9H0R8） MG MAGNESIUM ION × 3 PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 1 PER PEROXIDE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MgCl2, 24.6 % PEG 400, 29.5 % PEG 8000, 0.1M TRIS 8.5	Resolution 1.44 Å R-free 0.230

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 5LXI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CY7 The crystal structure of human Atg4B Deposited 2005-07-05	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 1–393（393 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；potassium phosphate, sodium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.247
2D1I Structure of human Atg4b Deposited 2005-08-24	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 1–393（393 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；0.65M tri-Sodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.00 Å R-free 0.283
2D1I Structure of human Atg4b Deposited 2005-08-24	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 1–393（393 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；0.65M tri-Sodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.00 Å R-free 0.283
2Z0D The crystal structure of human Atg4B- LC3(1-120) complex Deposited 2007-05-07	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 1–354（354 aa） Fragment：residues (-2)-354	Mutation：H280A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% PEG 3350, 0.1M sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.227
2Z0E The crystal structure of human Atg4B- LC3(1-124) complex Deposited 2007-05-07	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 1–354（354 aa） Fragment：residues (-2)-354	Mutation：H280A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% PEG 3350, 0.1M sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.229
2ZZP The crystal structure of human Atg4B(C74S)- LC3(1-124) complex Deposited 2009-02-22	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 1–354（354 aa） Fragment：residues in database 1-354	Mutation：C74S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% PEG 3350, 0.1M sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.05 Å R-free 0.251
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21	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 E 384–393（10 aa） Fragment：UNP residues 384-393	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol	Resolution 1.58 Å R-free 0.237
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21	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 F 384–393（10 aa） Fragment：UNP residues 384-393	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol	Resolution 1.58 Å R-free 0.237
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21	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 G 384–393（10 aa） Fragment：UNP residues 384-393	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol	Resolution 1.58 Å R-free 0.237

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ATG4B_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 384–393 Author chain E； PDBConstruct 1–10； UniProt 384–393

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5lxi
Deposition date deposition_date	2016-09-21
Structure title title	GABARAP-L1 ATG4B LIR Complex
Keywords keywords	LIR, GABARAP, ATG8, LC3, Signaling protein; SIGNALING PROTEIN
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	22.57 Å
Radius of gyration Rg (electron density) rg_electron	21.92 Å
Forward intensity I(0) i0	14679500.00
Molecular weight molecular_weight	29736.0 kDa
Excluded volume excluded_volume	37483 Å³
Envelope volume envelope_volume	45359 Å³
Hydration-shell volume shell_volume	18196 Å³
Envelope diameter envelope_diameter	74.8 Å
Shell Rg shell_rg	27.23 Å
Envelope Rg envelope_rg	21.99 Å
Shape Rg shape_rg	21.85 Å
Total Rg total_rg	22.86 Å
Total atoms total_atoms	2106
Residues n_residues	249
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	74.7 Å
Rg (real space) rg_real	22.66 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	1.4680e+07
I(0) uncertainty (real space) i0_real_error	1.8610e+05
Rg (reciprocal space) rg_reciprocal	22.64 Å
I(0) (reciprocal space) i0_reciprocal	14680000.0000
Solution quality estimate total_estimate	0.8677
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.6 Å
Skewness Skewness skewness	0.421
Kurtosis Kurtosis kurtosis	-0.504
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3690000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Gamma-aminobutyric acid receptor-associated protein-like 1
Molecular weight formula_weight	14598.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,B
Atom count atom_count	2290

GPTMGSMKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK

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	Cysteine protease ATG4B
Molecular weight formula_weight	1289.2 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E

EDEDFEILSL

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PEROXIDE ION
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5lxiB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	5lxiD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	124.888 Å
Unit-cell length b length_b	72.377 Å
Unit-cell length c length_c	30.620 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.440 Å
Low-resolution limit resolution_low	31.207 Å
R factor r_factor	0.1987
R_work r_work	0.1969
R_free r_free	0.2299

fit	/app/data/saxs_computation/lx/5lxi/5lxi.fit
pddf	/app/data/pr_computation/lx/5lxi/5lxi.pr.out
profile	/app/data/saxs_computation/lx/5lxi/5lxi.dat

GABARAP-L1 ATG4B LIR Complex

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

Gamma-aminobutyric acid receptor-associated protein-like 1

State in the Current Structure

Other States of the Same Protein in the Database

Cysteine protease ATG4B

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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)