8x8a

Crystal structure of STBD1 LIR motif in complex with GABARAPL1

Method: X-RAY DIFFRACTION D_max: 50.9 Å Quality: GOOD

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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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–117	Not recorded	Starch-binding domain-containing protein 1 × 1 （O95210）	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

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 8X8A	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
9HGC Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8 Deposited 2024-11-19	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 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 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 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 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 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 A； PDBConstruct 1–117； UniProt 1–117

Starch-binding domain-containing protein 1

Homo sapiens

UniProt O95210

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 B； UniProt 200–210	Fragment：LIR motif	Gamma-aminobutyric acid receptor-associated protein-like 1 × 1 （Q9H0R8）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8X8A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8X8K Crystal structure of STBD1 CBM20 domain in complex with maltotetraose Deposited 2023-11-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 260–358（99 aa） Fragment：CBM20 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (Imidazole; MES (acid) pH 6.5), 37.5% v/v Precipitant Mix 4 (25% v/v MPD (racemic); 25% PEG 1000; 25% w/v PEG 3350)	Resolution 2.10 Å R-free 0.226
8X8K Crystal structure of STBD1 CBM20 domain in complex with maltotetraose Deposited 2023-11-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 260–358（99 aa） Fragment：CBM20 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (Imidazole; MES (acid) pH 6.5), 37.5% v/v Precipitant Mix 4 (25% v/v MPD (racemic); 25% PEG 1000; 25% w/v PEG 3350)	Resolution 2.10 Å R-free 0.226
8X8K Crystal structure of STBD1 CBM20 domain in complex with maltotetraose Deposited 2023-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain C 260–358（99 aa） Fragment：CBM20 domain	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (Imidazole; MES (acid) pH 6.5), 37.5% v/v Precipitant Mix 4 (25% v/v MPD (racemic); 25% PEG 1000; 25% w/v PEG 3350)	Resolution 2.10 Å R-free 0.226
8X8K Crystal structure of STBD1 CBM20 domain in complex with maltotetraose Deposited 2023-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain D 260–358（99 aa） Fragment：CBM20 domain	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (Imidazole; MES (acid) pH 6.5), 37.5% v/v Precipitant Mix 4 (25% v/v MPD (racemic); 25% PEG 1000; 25% w/v PEG 3350)	Resolution 2.10 Å R-free 0.226

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

View Construct and Data Evidence

UniProt name	STBD1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–15； UniProt 200–210

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	8x8a
Deposition date deposition_date	2023-11-27
最后修订 last_revision	2024-09-18
Structure title title	Crystal structure of STBD1 LIR motif in complex with GABARAPL1
Keywords keywords	STBD1, LIR, GABARAPL1, 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	15.70 Å
Radius of gyration Rg (electron density) rg_electron	14.29 Å
Forward intensity I(0) i0	4488270.00
Molecular weight molecular_weight	15469.0 kDa
Excluded volume excluded_volume	19495 Å³
Envelope volume envelope_volume	21749 Å³
Hydration-shell volume shell_volume	12890 Å³
Envelope diameter envelope_diameter	50.6 Å
Shell Rg shell_rg	20.14 Å
Envelope Rg envelope_rg	14.67 Å
Shape Rg shape_rg	14.26 Å
Total Rg total_rg	15.57 Å
Total atoms total_atoms	1096
Residues n_residues	130
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	50.9 Å
Rg (real space) rg_real	15.59 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	4.4880e+06
I(0) uncertainty (real space) i0_real_error	4.6240e+04
Rg (reciprocal space) rg_reciprocal	15.61 Å
I(0) (reciprocal space) i0_reciprocal	4488000.0000
Solution quality estimate total_estimate	0.8765
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.138
Kurtosis Kurtosis kurtosis	-0.296
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1142000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.974

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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	Gamma-aminobutyric acid receptor-associated protein-like 1
Molecular weight formula_weight	14068.1 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	1285

MKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK

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

Entity 2 Entity 2 polymer

Description description	Starch-binding domain-containing protein 1
Molecular weight formula_weight	2026.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPGSHEEWEMVPRHSGSGS

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	144

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8. Citations (1)

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Unit-cell length a length_a	100.395 Å
Unit-cell length b length_b	100.395 Å
Unit-cell length c length_c	100.395 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	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	cubic

Resolution resolution	1.530 Å
Low-resolution limit resolution_low	25.100 Å
R factor r_factor	0.1735
R_work r_work	0.1727
R_free r_free	0.1868

fit	/app/data/saxs_computation/x8/8x8a/8x8a.fit
pddf	/app/data/pr_computation/x8/8x8a/8x8a.pr.out
profile	/app/data/saxs_computation/x8/8x8a/8x8a.dat

Crystal structure of STBD1 LIR motif in complex with GABARAPL1

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

Starch-binding domain-containing protein 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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)