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5dpr

Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121

Method: X-RAY DIFFRACTION Dmax: 88.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A

Homo sapiens

UniProt Q9H492

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 2–121 Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121 No other associated polymer 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
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 2–121 Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121 No other associated polymer 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
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 2–121 Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121 No other associated polymer 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
4 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 2–121 Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121 No other associated polymer 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

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 5DPR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3ECI Microtubule-associated protein 1 light chain 3 alpha isoform A (MAP1ALC3) Deposited 2008-08-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–121（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；32 % PEG 4000, 0.1 M NA ACETATE, PH 4.50, 0.2 M AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, CRYOPROTECTION 20% GLYCEROL, TEMPERATURE 298K
Resolution 2.65 Å R-free 0.304
3ECI Microtubule-associated protein 1 light chain 3 alpha isoform A (MAP1ALC3) Deposited 2008-08-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–121（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；32 % PEG 4000, 0.1 M NA ACETATE, PH 4.50, 0.2 M AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, CRYOPROTECTION 20% GLYCEROL, TEMPERATURE 298K
Resolution 2.65 Å R-free 0.304
3WAL Crystal structure of human LC3A_2-121 Deposited 2013-05-06 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 2–121（120 aa）
Not recorded MLT D-MALATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.2M Sodium malonate, 20% PEG 3350, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.237
3WAN Crystal structure of Atg13 LIR-fused human LC3A_2-121 Deposited 2013-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–121（120 aa） Fragment：UNP RESIDUES 436-447, 2-121
Chain B 2–121（120 aa） Fragment：UNP RESIDUES 436-447, 2-121
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；12% MPD, 0.1M Sodium chloride, 0.1M Sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.77 Å R-free 0.227
4ZDV Crystal structure of LC3 in complex with FAM134B LIR Deposited 2015-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–120（119 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8% Tacsimate (Hampton Research) pH 8.0, 20% Poly ethylene glycol 3350
Resolution 1.80 Å R-free 0.223
5CX3 Crystal structure of FYCO1 LIR in complex with LC3A Deposited 2015-07-28 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 A 1–121（121 aa）
Chain C 1–121（121 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；289 K；1.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES sodium
Resolution 2.30 Å R-free 0.244
5CX3 Crystal structure of FYCO1 LIR in complex with LC3A Deposited 2015-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–121（121 aa）
Chain D 1–121（121 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；289 K；1.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES sodium
Resolution 2.30 Å R-free 0.244
5CX3 Crystal structure of FYCO1 LIR in complex with LC3A Deposited 2015-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–121（121 aa）
Chain B 1–121（121 aa）
Chain C 1–121（121 aa）
Chain D 1–121（121 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；289 K；1.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES sodium
Resolution 2.30 Å R-free 0.244
6TBE LC3A in complex with (3R,4S,5R,6R)-5-hydroxy-6-((4-hydroxy-3-(4-hydroxy-3-isopentylbenzamido)-8-methyl-2-oxo-2H-chromen-7-yl)oxy)-3-methoxy-2,2-dimethyltetrahydro-2H-pyran-4-yl carbamate Deposited 2019-11-01 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 4–119（116 aa）
Not recorded NOV NOVOBIOCIN × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M ammoniumnitrat and 20% w/v PEG 3350
Resolution 1.67 Å R-free 0.212
7R9W LC3A in complex with Fragment 1-1 Deposited 2021-06-29 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 1–120（120 aa）
Not recorded JO4 4-phenoxybenzoic acid × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Sodium formate, 20% PEG 3350
Resolution 1.75 Å R-free 0.213
7R9Z LC3A in complex with Fragment 2-3 Deposited 2021-06-29 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 1–120（120 aa）
Not recorded 2LZ (5-fluoro-1H-indol-3-yl)acetic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Sodium formate, 20% PEG 3350
Resolution 1.72 Å R-free 0.218
7RA0 LC3A in complex with Fragment 2-10 Deposited 2021-06-29 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 1–120（120 aa）
Not recorded 2JI (5-ethyl-2-methyl-1H-indol-3-yl)acetic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Sodium formate, 20% PEG 3350
Resolution 1.36 Å R-free 0.201
8T2L Crystal structure of LC3A in complex with the LIR of NSs4 Deposited 2023-06-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–121（121 aa） Fragment：GS is the remain of the removed expression tag. The N terminus of Nss has been fused with Q9H492 to facilitate the crystalization.
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M Na-citrate, 5% Isopropanol, 0.1M MES buffer PH 6.5
Resolution 2.24 Å R-free 0.276
8T2L Crystal structure of LC3A in complex with the LIR of NSs4 Deposited 2023-06-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–121（121 aa） Fragment：GS is the remain of the removed expression tag. The N terminus of Nss has been fused with Q9H492 to facilitate the crystalization.
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M Na-citrate, 5% Isopropanol, 0.1M MES buffer PH 6.5
Resolution 2.24 Å R-free 0.276
8T35 Crystal structure of K51 acetylated LC3A in complex with the LIR of TP53INP2/DOR Deposited 2023-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–121（121 aa）
Chain B 1–121（121 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG4000, 0.1M Na-citrate pH 5.5
Resolution 1.90 Å R-free 0.259
8T36 Crystal structure of K49 acetylated LC3A in complex with the LIR of TP53INP2/DOR Deposited 2023-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–121（121 aa） Fragment：;GS is the remain of the removed expression tag. TP53INP2 Q8IXH6 peptide is fused to the N- terminal of the Q9H492 to facilitate the crystallization. ;
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG3350, 0.1M Na-citrate, 5% isopropanol, 0.1 M HEPES pH 7.5
Resolution 1.85 Å R-free 0.258
8T4T Crystal structure of LC3A in complex with the LIR of TP53INP2/DOR Deposited 2023-06-10 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–121（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12.5% PEG3350, 0.2M NH4-citrate, 5% isopropanol, 0.1M MES pH6.5
Resolution 2.36 Å R-free 0.272
8T4T Crystal structure of LC3A in complex with the LIR of TP53INP2/DOR Deposited 2023-06-10 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–121（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12.5% PEG3350, 0.2M NH4-citrate, 5% isopropanol, 0.1M MES pH6.5
Resolution 2.36 Å R-free 0.272

13 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MLP3A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 17–136； UniProt 2–121 Author chain B； PDBConstruct 17–136； UniProt 2–121 Author chain C； PDBConstruct 17–136； UniProt 2–121 Author chain D； PDBConstruct 17–136； UniProt 2–121

Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A

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 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121 No other associated polymer 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
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 627–638 Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121 No other associated polymer 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
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 627–638 Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121 No other associated polymer 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
4 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 627–638 Fragment：UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121,UNP Q9Y4G2 residues 627-638, UNP Q9H492 residues 2-121 No other associated polymer 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

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 5DPR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5DPS Crystal structure of PLEKHM1 LIR-fused human GABARAP_2-117 Deposited 2015-09-14 Different construct 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 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 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
5DPT Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_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 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 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 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
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14 Different construct Different oligomeric state 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 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 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 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 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 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 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 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 15 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 Author chain C； PDBConstruct 3–14； UniProt 627–638 Author chain D； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 5dpr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5dpr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5dpr
Deposition date deposition_date2015-09-14
Structure title titleCrystal structure of PLEKHM1 LIR-fused human LC3A_2-121
Keywords keywordsAutophagy; PLEKHM1; Atg8; LC3; GABARAP, chimeric protein, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.76 Å
Radius of gyration Rg (electron density) rg_electron27.83 Å
Forward intensity I(0) i054921800.00
Molecular weight molecular_weight57904.0 kDa
Excluded volume excluded_volume72792 ų
Envelope volume envelope_volume103000 ų
Hydration-shell volume shell_volume31422 ų
Envelope diameter envelope_diameter90.6 Å
Shell Rg shell_rg34.70 Å
Envelope Rg envelope_rg26.66 Å
Shape Rg shape_rg27.81 Å
Total Rg total_rg28.70 Å
Total atoms total_atoms8115
Residues n_residues502
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax88.0 Å
Rg (real space) rg_real28.64 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real5.4920e+07
I(0) uncertainty (real space) i0_real_error8.2520e+05
Rg (reciprocal space) rg_reciprocal28.69 Å
I(0) (reciprocal space) i0_reciprocal54920000.0000
Solution quality estimate total_estimate0.9122
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.8 Å
Skewness Skewness skewness0.109
Kurtosis Kurtosis kurtosis-0.581
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6642000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.962
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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5dpra_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.3 — GABARAP-like
Domain ID domain_idd5dprb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.3 — GABARAP-like
Domain ID domain_idd5dprc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.3 — GABARAP-like
Domain ID domain_idd5dprd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.3 — GABARAP-like

CATH v4.4 (4 domains)

Domain ID domain_id5dprA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id5dprB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id5dprC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id5dprD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)