SAXSdb — 5dpt

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

;Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,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	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–117	Fragment：UNP Q9Y4G2 627-638, UNP Q9H0R8 2-117	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
2	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–117	Fragment：UNP Q9Y4G2 627-638, UNP Q9H0R8 2-117	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

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 5DPT	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 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 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 oligomeric state 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
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21	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 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 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 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
5LXI 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 × 4 PDB declaration: tetrameric	Chain B 1–117（117 aa） Chain D 1–117（117 aa）	Not recorded	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
6HOI Structure of Beclin1 LIR motif bound to GABARAPL1 Deposited 2018-09-17	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 29 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 A； PDBConstruct 17–132； UniProt 2–117 Author chain B； PDBConstruct 17–132； UniProt 2–117

;Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1 ;

Homo sapiens

UniProt Q9Y4G2

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 627–638	Fragment：UNP Q9Y4G2 627-638, UNP Q9H0R8 2-117	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
2	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 627–638	Fragment：UNP Q9Y4G2 627-638, UNP Q9H0R8 2-117	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

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 5DPT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5DPR Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121 Deposited 2015-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 627–638（12 aa） Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；278 K；0.2 M ammonium acetate, 0.1 M Bis Tris, pH 5.5, 25% w/v Polyethlene glycol 3,350	Resolution 2.50 Å R-free 0.261
5DPR Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121 Deposited 2015-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 627–638（12 aa） Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；278 K；0.2 M ammonium acetate, 0.1 M Bis Tris, pH 5.5, 25% w/v Polyethlene glycol 3,350	Resolution 2.50 Å R-free 0.261
5DPR Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121 Deposited 2015-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 627–638（12 aa） Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；278 K；0.2 M ammonium acetate, 0.1 M Bis Tris, pH 5.5, 25% w/v Polyethlene glycol 3,350	Resolution 2.50 Å R-free 0.261
5DPR Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121 Deposited 2015-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 627–638（12 aa） Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；278 K；0.2 M ammonium acetate, 0.1 M Bis Tris, pH 5.5, 25% w/v Polyethlene glycol 3,350	Resolution 2.50 Å R-free 0.261
5DPS Crystal structure of PLEKHM1 LIR-fused human GABARAP_2-117 Deposited 2015-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 627–638（12 aa） Fragment：UNP Q9Y4G2 residues 627-638, UNP O95166 residues 2-117	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；278 K；4% v/v Tacsimate pH 8.0, 12% w/v Polyethylene glycol 3,350	Resolution 2.00 Å R-free 0.223
5DPS Crystal structure of PLEKHM1 LIR-fused human GABARAP_2-117 Deposited 2015-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 627–638（12 aa） Fragment：UNP Q9Y4G2 residues 627-638, UNP O95166 residues 2-117	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；278 K；4% v/v Tacsimate pH 8.0, 12% w/v Polyethylene glycol 3,350	Resolution 2.00 Å R-free 0.223
5DPS Crystal structure of PLEKHM1 LIR-fused human GABARAP_2-117 Deposited 2015-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 627–638（12 aa） Fragment：UNP Q9Y4G2 residues 627-638, UNP O95166 residues 2-117	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；278 K；4% v/v Tacsimate pH 8.0, 12% w/v Polyethylene glycol 3,350	Resolution 2.00 Å R-free 0.223
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	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 B 629–642（14 aa） Fragment：UNP residues 629-642	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	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 D 629–642（14 aa） Fragment：UNP residues 629-642	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 629–642（14 aa） Fragment：UNP residues 629-642	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 629–642（14 aa） Fragment：UNP residues 629-642	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 629–642（14 aa） Fragment：UNP residues 629-642	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 629–642（14 aa） Fragment：UNP residues 629-642	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 629–642（14 aa） Fragment：UNP residues 629-642	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 629–642（14 aa） Fragment：UNP residues 629-642	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
8JC5 Crystal structure of PLEKHM1 RUN domain in complex with GTP-bound Arl8b(Q75L) Deposited 2023-05-10	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 D 10–205（196 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Lithium chloride, 0.1 M TRIS pH=7.6, 18% (w/v) PEG 8000	Resolution 2.01 Å R-free 0.201
8JC5 Crystal structure of PLEKHM1 RUN domain in complex with GTP-bound Arl8b(Q75L) Deposited 2023-05-10	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 C 10–205（196 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Lithium chloride, 0.1 M TRIS pH=7.6, 18% (w/v) PEG 8000	Resolution 2.01 Å R-free 0.201

4 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PKHM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–14； UniProt 627–638 Author chain B； PDBConstruct 3–14； UniProt 627–638

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	5dpt
Deposition date deposition_date	2015-09-14
Structure title title	Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117
Keywords keywords	Autophagy, chimeric protein, PROTEIN BINDING; PROTEIN BINDING
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	20.46 Å
Radius of gyration Rg (electron density) rg_electron	19.48 Å
Forward intensity I(0) i0	12876800.00
Molecular weight molecular_weight	27392.0 kDa
Excluded volume excluded_volume	34444 Å³
Envelope volume envelope_volume	42612 Å³
Hydration-shell volume shell_volume	18584 Å³
Envelope diameter envelope_diameter	70.4 Å
Shell Rg shell_rg	25.31 Å
Envelope Rg envelope_rg	19.79 Å
Shape Rg shape_rg	19.47 Å
Total Rg total_rg	20.42 Å
Total atoms total_atoms	1949
Residues n_residues	245
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	67.1 Å
Rg (real space) rg_real	20.42 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.2880e+07
I(0) uncertainty (real space) i0_real_error	1.5680e+05
Rg (reciprocal space) rg_reciprocal	20.43 Å
I(0) (reciprocal space) i0_reciprocal	12880000.0000
Solution quality estimate total_estimate	0.8132
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.305
Kurtosis Kurtosis kurtosis	-0.290
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2325000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5dpta_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d5dptb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5dptA00
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	5dptB00
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	84.791 Å
Unit-cell length b length_b	84.791 Å
Unit-cell length c length_c	105.440 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	42.826 Å
R factor r_factor	0.2162
R_work r_work	0.2140
R_free r_free	0.2595

Description description	;Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1 ;
Molecular weight formula_weight	15706.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1949

Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117

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

;Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1 ;

State in the Current Structure

Other States of the Same Protein in the Database

;Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1 ;

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

fit	/app/data/saxs_computation/dp/5dpt/5dpt.fit
pddf	/app/data/pr_computation/dp/5dpt/5dpt.pr.out
profile	/app/data/saxs_computation/dp/5dpt/5dpt.dat