5dpw

Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125

Method: X-RAY DIFFRACTION D_max: 118.9 Å Quality: REASONABLE

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

Microtubule-associated proteins 1A/1B light chain 3C

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 8–125	Fragment：UNP residues 8-125	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 8–125	Fragment：UNP residues 8-125	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2）	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 8–125	Fragment：UNP residues 8-125	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2）	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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 8–125	Fragment：UNP residues 8-125	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2）	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
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain I； UniProt 8–125	Fragment：UNP residues 8-125	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2）	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
6	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain K； UniProt 8–125	Fragment：UNP residues 8-125	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2）	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
7	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain M； UniProt 8–125	Fragment：UNP residues 8-125	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2）	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
8	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain O； UniProt 8–125	Fragment：UNP residues 8-125	Pleckstrin homology domain-containing family M member 1 × 1 （Q9Y4G2）	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

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 5DPW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NCN Solution Structure of the Autophagy-Related Protein LC3C Deposited 2016-04-11	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–126（126 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293.15 K；Ionic strength (raw mmCIF value) 171；Pressure 1 NMR sample composition 0.35-0.7 mM [U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 90% H2O, 10% D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35-0.7 mM [U-13C; U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 90% H2O, 10% D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35-0.7 mM [U-13C; U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 100% D2O, 100% D2O \| 100% D2O	Resolution not provided
3VVW NDP52 in complex with LC3C Deposited 2012-07-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–126（126 aa） Fragment：UNP residues 1-126	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；16% PEG6000, 0.01M sodium citrate , pH 7.0, Vapor Diffusion, temperature 293K	Resolution 2.50 Å R-free 0.252
3WAM Crystal structure of human LC3C_8-125 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 8–125（118 aa） Fragment：UNP RESIDUES 8-125	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.5M di-Ammonium hydrogen citrate, 10% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.211
3WAM Crystal structure of human LC3C_8-125 Deposited 2013-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 8–125（118 aa） Fragment：UNP RESIDUES 8-125	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.5M di-Ammonium hydrogen citrate, 10% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.211
3WAP Crystal structure of Atg13 LIR-fused human LC3C_8-125 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 8–125（118 aa） Fragment：UNP RESIDUES 436-447, 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M Sodium acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.273
3WAP Crystal structure of Atg13 LIR-fused human LC3C_8-125 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 8–125（118 aa） Fragment：UNP RESIDUES 436-447, 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M Sodium acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.273

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

View Construct and Data Evidence

UniProt name	MLP3C_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–118； UniProt 8–125 Author chain C； PDBConstruct 1–118； UniProt 8–125 Author chain E； PDBConstruct 1–118； UniProt 8–125 Author chain G； PDBConstruct 1–118； UniProt 8–125 Author chain I； PDBConstruct 1–118； UniProt 8–125 Author chain K； PDBConstruct 1–118； UniProt 8–125 Author chain M； PDBConstruct 1–118； UniProt 8–125 Author chain O； PDBConstruct 1–118； UniProt 8–125

Pleckstrin homology domain-containing family M member 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	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 629–642	Fragment：UNP residues 629-642	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 629–642	Fragment：UNP residues 629-642	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4）	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 629–642	Fragment：UNP residues 629-642	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4）	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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 629–642	Fragment：UNP residues 629-642	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4）	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
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain J； UniProt 629–642	Fragment：UNP residues 629-642	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4）	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
6	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 629–642	Fragment：UNP residues 629-642	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4）	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
7	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain N； UniProt 629–642	Fragment：UNP residues 629-642	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4）	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
8	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain P； UniProt 629–642	Fragment：UNP residues 629-642	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5DPW	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
8JC5 Crystal structure of PLEKHM1 RUN domain in complex with GTP-bound Arl8b(Q75L) Deposited 2023-05-10	Different construct 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 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 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PKHM1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–14； UniProt 629–642 Author chain D； PDBConstruct 1–14； UniProt 629–642 Author chain F； PDBConstruct 1–14； UniProt 629–642 Author chain H； PDBConstruct 1–14； UniProt 629–642 Author chain J； PDBConstruct 1–14； UniProt 629–642 Author chain L； PDBConstruct 1–14； UniProt 629–642 Author chain N； PDBConstruct 1–14； UniProt 629–642 Author chain P； PDBConstruct 1–14； UniProt 629–642

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	5dpw
Deposition date deposition_date	2015-09-14
Structure title title	Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125
Keywords keywords	Autophagy, 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	36.85 Å
Radius of gyration Rg (electron density) rg_electron	36.11 Å
Forward intensity I(0) i0	194444000.00
Molecular weight molecular_weight	117250.0 kDa
Excluded volume excluded_volume	148850 Å³
Envelope volume envelope_volume	203430 Å³
Hydration-shell volume shell_volume	46594 Å³
Envelope diameter envelope_diameter	126.7 Å
Shell Rg shell_rg	43.15 Å
Envelope Rg envelope_rg	35.11 Å
Shape Rg shape_rg	36.11 Å
Total Rg total_rg	36.60 Å
Total atoms total_atoms	16597
Residues n_residues	992
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	118.9 Å
Rg (real space) rg_real	36.69 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	1.9440e+08
I(0) uncertainty (real space) i0_real_error	3.2540e+06
Rg (reciprocal space) rg_reciprocal	36.79 Å
I(0) (reciprocal space) i0_reciprocal	194500000.0000
Solution quality estimate total_estimate	0.6769
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.8 Å
Skewness Skewness skewness	0.098
Kurtosis Kurtosis kurtosis	-0.530
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25040000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.998; Smooth: 0.963

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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	Microtubule-associated proteins 1A/1B light chain 3C
Molecular weight formula_weight	13808.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	16830

PSVRPFKQRKSLAIRQEEVAGIRAKFPNKIPVVVERYPRETFLPPLDKTKFLVPQELTMTQFLSIIRSRMVLRATEAFYLLVNNKSLVSMSATMAEIYRDYKDEDGFVYMTYASQETF

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	Pleckstrin homology domain-containing family M member 1
Molecular weight formula_weight	1746.8 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P

PQQEDEWVNVQYPD

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	160

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5dpwa_
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.15.1.3 — GABARAP-like

Domain ID domain_id	d5dpwc_
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.15.1.3 — GABARAP-like

Domain ID domain_id	d5dpwe_
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.15.1.3 — GABARAP-like

Domain ID domain_id	d5dpwg_
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.15.1.3 — GABARAP-like

Domain ID domain_id	d5dpwi_
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.15.1.3 — GABARAP-like

Domain ID domain_id	d5dpwk_
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.15.1.3 — GABARAP-like

Domain ID domain_id	d5dpwm_
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.15.1.3 — GABARAP-like

Domain ID domain_id	d5dpwo_
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.15.1.3 — GABARAP-like

CATH v4.4 (8 domains)

Domain ID domain_id	5dpwA00
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	5dpwC00
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	5dpwE00
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	5dpwG00
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	5dpwI00
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	5dpwK00
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	5dpwM00
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	5dpwO00
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	54.140 Å
Unit-cell length b length_b	73.225 Å
Unit-cell length c length_c	89.048 Å
Unit-cell angle α angle_alpha	89.96 °
Unit-cell angle β angle_beta	89.99 °
Unit-cell angle γ angle_gamma	77.31 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.185 Å
Low-resolution limit resolution_low	38.610 Å
R factor r_factor	0.2006
R_work r_work	0.1996
R_free r_free	0.2457

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

Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125

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

Microtubule-associated proteins 1A/1B light chain 3C

State in the Current Structure

Other States of the Same Protein in the Database

Pleckstrin homology domain-containing family M member 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

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)