5d94

Crystal structure of LC3-LIR peptide complex

Method: X-RAY DIFFRACTION D_max: 50.2 Å Quality: GOOD

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

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

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 1–125	Not recorded	Peptide from FYVE and coiled-coil domain-containing protein 1 × 1 （Q9BQS8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Potassium thiocyanate, 30%(w/v) Polyethylene glycol monomethyl ether 2000	Resolution 1.53 Å R-free 0.215

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 5D94	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1V49 Solution structure of microtubule-associated protein light chain-3 Deposited 2003-11-11	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 0–119（120 aa） Fragment：residues 1-120	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 230；Pressure 1 NMR sample composition 0.8mM protein U-15N, 13C; 25mM phosphate buffer NA; 100mM NACL; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8mM protein U-15N, 13C; 25mM phosphate buffer NA; 100mM NACL; 100% D2O \| 100% D2O	Resolution not provided
2LUE LC3B OPTN-LIR Ptot complex structure Deposited 2012-06-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 5–119（115 aa） Fragment：UNP RESIDUES 5-119	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；288 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 0.6 mM [U-98% 13C; U-98% 15N] entity_1-1, 4.9 mM entity_2-2, 70 mM sodium phosphate-3, 30 mM sodium chloride-4, 0.3 mM DSS-5, 5 mM Protease inhibitors cocktail-6, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 2.5 mM [U-98% 13C; U-98% 15N] entity_1-7, 0.4 mM entity_2-8, 70 mM sodium phosphate-9, 30 mM sodium chloride-10, 0.3 mM DSS-11, 5 mM Protease inhibitors cocktail-12, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2N9X LC3 FUNDC1 complex structure Deposited 2015-12-14	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition 0.9 mM [U-13C; U-15N] entity_1-1, 1.8 mM entity_2-2, 100 mM sodium chloride-3, 25 mM sodium phosphate-4, 10 % [U-2H] D2O-5, 1 % DSS-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2ZJD Crystal Structure of LC3-p62 complex Deposited 2008-03-05	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES pH 7.5, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.56 Å R-free 0.238
2ZJD Crystal Structure of LC3-p62 complex Deposited 2008-03-05	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–125（125 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES pH 7.5, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.56 Å R-free 0.238
2ZJD Crystal Structure of LC3-p62 complex Deposited 2008-03-05	Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES pH 7.5, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.56 Å R-free 0.238
2ZJD Crystal Structure of LC3-p62 complex Deposited 2008-03-05	Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–125（125 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.1M HEPES pH 7.5, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.56 Å R-free 0.238
3VTU Crystal structure of human LC3B_2-119 Deposited 2012-06-08	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 2–119（118 aa） Fragment：UNP RESIDUES 2-119	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；2.0M Ammonium sulfate, 0.1M Tri-sodium citrate, 0.2M Potassium sodium tartrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.231
3VTV Crystal structure of Optineurin LIR-fused human LC3B_2-119 Deposited 2012-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–119（118 aa） Fragment：UNP RESIDUES 170-181, RESIDUES 2-119	Mutation：S170E, S171E, S173E, S174E, S177E	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；2.0M Ammonium sulfate, 0.05M Tri-sodium citrate, 0.1M Potassium sodium tartrate, 10% PEG 3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.70 Å R-free 0.252
3VTW Crystal structure of T7-tagged Optineurin LIR-fused human LC3B_2-119 Deposited 2012-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–119（118 aa） Fragment：UNP RESIDUES 170-181, RESIDUES 2-119	Mutation：S170E, S171E, S173E, S174E, S177E	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；2.0M Ammonium sulfate, 0.05M Tri-sodium citrate, 0.1M Potassium sodium tartrate, 5% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.52 Å R-free 0.280
3VTW Crystal structure of T7-tagged Optineurin LIR-fused human LC3B_2-119 Deposited 2012-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–119（118 aa） Fragment：UNP RESIDUES 170-181, RESIDUES 2-119	Mutation：S170E, S171E, S173E, S174E, S177E	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；2.0M Ammonium sulfate, 0.05M Tri-sodium citrate, 0.1M Potassium sodium tartrate, 5% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.52 Å R-free 0.280
3VTW Crystal structure of T7-tagged Optineurin LIR-fused human LC3B_2-119 Deposited 2012-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–119（118 aa） Fragment：UNP RESIDUES 170-181, RESIDUES 2-119	Mutation：S170E, S171E, S173E, S174E, S177E	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；2.0M Ammonium sulfate, 0.05M Tri-sodium citrate, 0.1M Potassium sodium tartrate, 5% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.52 Å R-free 0.280
3WAO Crystal structure of Atg13 LIR-fused human LC3B_2-119 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 2–119（118 aa） Fragment：RESIDUES 436-447, RESIDUES 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium citrate tribasic dihydrate 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.294
3WAO Crystal structure of Atg13 LIR-fused human LC3B_2-119 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–119（118 aa） Fragment：RESIDUES 436-447, RESIDUES 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium citrate tribasic dihydrate 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.294
3WAO Crystal structure of Atg13 LIR-fused human LC3B_2-119 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–119（118 aa） Fragment：RESIDUES 436-447, RESIDUES 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium citrate tribasic dihydrate 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.294
3WAO Crystal structure of Atg13 LIR-fused human LC3B_2-119 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2–119（118 aa） Fragment：RESIDUES 436-447, RESIDUES 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium citrate tribasic dihydrate 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.294
3X0W Crystal structure of PLEKHM1 LIR-fused human LC3B_2-119 Deposited 2014-10-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–119（118 aa） Fragment：UNP RESIDUES 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M Acetate, pH 5.0, 1.4M Ammonium Sulfate, 0.1M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.71 Å R-free 0.294
3X0W Crystal structure of PLEKHM1 LIR-fused human LC3B_2-119 Deposited 2014-10-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–119（118 aa） Fragment：UNP RESIDUES 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M Acetate, pH 5.0, 1.4M Ammonium Sulfate, 0.1M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.71 Å R-free 0.294
4WAA Crystal structure of Nix LIR-fused human LC3B_2-119 Deposited 2014-08-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Monomeric	Chain A 2–119（118 aa） Fragment：UNP residues 2-119 Chain B 2–119（118 aa） Fragment：UNP residues 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；300 K；20% PEG3350, 8% Tacsimate pH 4	Resolution 2.35 Å R-free 0.273
5DCN Crystal structure of LC3 in complex with TECPR2 LIR Deposited 2015-08-24	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 2–119（118 aa） Fragment：UNP residues 2-119	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.8M Lithium sulphate, 0.01M Magnesium chloride, 0.05M MES monohydrate, pH5.6	Resolution 2.00 Å R-free 0.247
5GMV LC3B-FUNDC1 complex Deposited 2016-07-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–125（125 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG MME 2000, 0.1mM sodium cacodylate (pH 6.0)	Resolution 2.25 Å R-free 0.272
5GMV LC3B-FUNDC1 complex Deposited 2016-07-17	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG MME 2000, 0.1mM sodium cacodylate (pH 6.0)	Resolution 2.25 Å R-free 0.272
5MS2 Crystal structure of the Legionella pneumophila effector protein RavZ in complex with human LC3B Deposited 2016-12-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–119（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277.15 K；0.17 M ammonium acetate, 0.085M tri sodium citrate, 25.5% PEG 4000 and 15% glycerol	Resolution 2.47 Å R-free 0.238
5MS5 Low-salt structure of RavZ LIR2-fused human LC3B Deposited 2016-12-31	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 2–119（118 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M citric acid anhydrous and 1.6 M ammonium sulfate	Resolution 1.53 Å R-free 0.242
5MS5 Low-salt structure of RavZ LIR2-fused human LC3B Deposited 2016-12-31	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 2–119（118 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M citric acid anhydrous and 1.6 M ammonium sulfate	Resolution 1.53 Å R-free 0.242
5MS6 High-salt structure of RavZ LIR2-fused human LC3B Deposited 2016-12-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–119（118 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M sodium acetate and 3 M NaCl	Resolution 1.90 Å R-free 0.261
5MS6 High-salt structure of RavZ LIR2-fused human LC3B Deposited 2016-12-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–119（118 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M sodium acetate and 3 M NaCl	Resolution 1.90 Å R-free 0.261
5V4K Crystal structure of NEDD4 LIR-fused human LC3B_2-119 Deposited 2017-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–119（118 aa） Fragment：UNP residues 2-119,UNP residues 2-119,UNP residues 2-119,UNP residues 2-119 Chain B 2–119（118 aa） Fragment：UNP residues 2-119,UNP residues 2-119,UNP residues 2-119,UNP residues 2-119	Not recorded	GOL GLYCEROL × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1M Sodium Acetate pH 5.0, 1.2M Ammonium Sulfate	Resolution 2.10 Å R-free 0.233
5W9A The structure of the Trim5alpha Bbox- coiled coil in complex LC3B Deposited 2017-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 4–117（114 aa） Fragment：UNP residues 2-119 Chain D 4–117（114 aa） Fragment：UNP residues 2-119	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.2 M NH4Cl, 0.1 M Tris pH8, 20% PEG 6,000	Resolution 2.74 Å R-free 0.274
5XAC CLIR - LC3B Deposited 2017-03-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–120（119 aa） Chain B 2–120（119 aa） Chain C 2–120（119 aa） Chain D 2–120（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 3,350, 0.1M HEPES pH 7.5, 200mM NaCl.	Resolution 1.70 Å R-free 0.245
5XAD NLIR - LC3B fusion protein Deposited 2017-03-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–120（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；1.0 M Ammonium sulfate, 100mM CHES/NaOH pH 9.5, 200mM NaCl.	Resolution 1.88 Å R-free 0.253
5XAD NLIR - LC3B fusion protein Deposited 2017-03-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–120（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；1.0 M Ammonium sulfate, 100mM CHES/NaOH pH 9.5, 200mM NaCl.	Resolution 1.88 Å R-free 0.253
5XAE mutNLIR_LC3B Deposited 2017-03-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–120（119 aa） Chain B 2–120（119 aa） Chain C 2–120（119 aa） Chain D 2–120（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Pentaerythritol propoxylate, 0.1M HEPES pH 7.0, 0.2M Potassium chloride.	Resolution 2.00 Å R-free 0.259
6J04 Crystal structure of full length human LC3B delta G120 mutant (2_125) Deposited 2018-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–125（124 aa） Fragment：UNP residues 2-125 Chain C 2–125（124 aa） Fragment：UNP residues 2-125	Mutation：deletion mutant G120 Mutation：deletion mutant G120	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.16M ammonium sulfate, 0.08M sodium acetate pH4.6, 20% (w/v) PEG4000; 20% (v/v) glycerol	Resolution 1.90 Å R-free 0.262
6J04 Crystal structure of full length human LC3B delta G120 mutant (2_125) Deposited 2018-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2–125（124 aa） Fragment：UNP residues 2-125 Chain D 2–125（124 aa） Fragment：UNP residues 2-125	Mutation：deletion mutant G120 Mutation：deletion mutant G120	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.16M ammonium sulfate, 0.08M sodium acetate pH4.6, 20% (w/v) PEG4000; 20% (v/v) glycerol	Resolution 1.90 Å R-free 0.262
6LAN Structure of CCDC50 and LC3B complex Deposited 2019-11-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–125（124 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；20% v/v 2-Propanol, 0.1 M sodium citrate pH 5.6, 20% w/v PEG 2000 MME	Resolution 1.41 Å R-free 0.219
7ELG LC3B modificated with a covalent probe Deposited 2021-04-10	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 2–119（118 aa）	Not recorded	8Z6 2-methylidene-5-thiophen-2-yl-cyclohexane-1,3-dione × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；2.0M ammonium sulfate, 0.1M tri-sodium citrate (pH 5.6), 0.2M potassium sodium tartrate	Resolution 1.60 Å R-free 0.231
7GA8 PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1198158918 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	K4R 1H-indazole-3-carbonitrile × 1 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.87 Å R-free 0.274
7GA9 PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1198177230 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	K6U (2M)-2-(2-methoxyphenyl)-1,3,4-oxadiazole × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 2.17 Å R-free 0.246
7GAA PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1198233191 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	K7L (4S)-imidazo[1,2-a]pyrimidine-5,7-diol × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 2.03 Å R-free 0.248
7GAB PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1255402624 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	EYK 2-tert-butylbenzene-1,4-diol × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 2.23 Å R-free 0.276
7GAC PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1456069604 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	KF8 N-[(3S)-piperidin-3-yl]benzamide × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.91 Å R-free 0.260
7GAD PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1667545918 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	K8L N-[(1,3-thiazol-5-yl)methyl]acetamide × 2 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.86 Å R-free 0.258
7GAE PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1688504114 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	GV4 2-cyano-~{N}-(1,3,5-trimethylpyrazol-4-yl)ethanamide × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.92 Å R-free 0.251
7GAF PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z183352334 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	K96 N-{[(2R)-oxolan-2-yl]methyl}morpholine-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.84 Å R-free 0.245
7GAG PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z198195770 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	LJA N-[3-(carbamoylamino)phenyl]acetamide × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.59 Å R-free 0.215
7GAH PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z2033637875 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	LRF N~2~-(4-cyano-3-methyl-1,2-thiazol-5-yl)-N~2~-methylglycinamide × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.90 Å R-free 0.254
7GAI PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z212122838 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	K9N N-[(4-methyl-1,3-thiazol-2-yl)methyl]cyclobutanecarboxamide × 1 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.97 Å R-free 0.281
7GAJ PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z285233820 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	KB3 (5M)-5-(2-methoxyphenyl)-1,3,4-oxadiazol-2-amine × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.89 Å R-free 0.229
7GAK PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z287121492 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	KA3 N-(cyclopropylmethyl)-4-methoxypiperidine-1-carboxamide × 1 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.77 Å R-free 0.250
7GAL PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z291279160 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	LV4 1-[2-(trifluoromethyloxy)phenyl]thiourea × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.91 Å R-free 0.251
7GAM PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z373768900 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	NUA N-(1-ethyl-1H-pyrazol-4-yl)cyclobutanecarboxamide × 1 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.75 Å R-free 0.234
7GAN PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z56767614 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	RWP methyl 4-[(trifluoroacetyl)amino]benzoate × 1 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 2.09 Å R-free 0.256
7GAO PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z57450788 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	RV4 N-{4-[(morpholin-4-yl)methyl]phenyl}acetamide × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.69 Å R-free 0.218
7GAP PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z728939702 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	KCC N-methylquinoxalin-2-amine × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.68 Å R-free 0.244
7GAQ PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z755044716 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	K0J N-ethyl-1H-1,2,3-triazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 2.14 Å R-free 0.244
7GAR PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z820676436 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	2NU 2-(4-bromanylpyrazol-1-yl)-~{N}-cyclopropyl-~{N}-methyl-ethanamide × 1 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 2.07 Å R-free 0.264
7GAS PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z952016136 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	KBU 4-chloro-1H-benzimidazole × 1 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.91 Å R-free 0.276
7GAU PanDDA analysis group deposition of ground-state model of MAP1LC3B Deposited 2023-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：TruncationafterGly120	EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.59 Å R-free 0.217
8Q53 Crystal structure of truncated human Microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B) in apo form Deposited 2023-08-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：Truncation after Gly120	EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；293 K；36% PEG 8000, 0.1M acetate pH 4.7	Resolution 1.36 Å R-free 0.210
8Q7K IRGQ LIR2 peptide in complex with LC3B Deposited 2023-08-16	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；1 M lithium chloride, 0.1 M citrate, 20% PEG 6000	Resolution 1.60 Å R-free 0.213
8Q7K IRGQ LIR2 peptide in complex with LC3B Deposited 2023-08-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–125（125 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；1 M lithium chloride, 0.1 M citrate, 20% PEG 6000	Resolution 1.60 Å R-free 0.213
8YV6 Crystal structure of LC3B in complex with Influenza A virus M2 peptide Deposited 2024-03-28	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% Jeffamine, 0.1M HEPES, pH 7.0	Resolution 1.75 Å R-free 0.250
9VUY NMR Structure of LC3B in complex with HBx BH3-like motif Deposited 2025-07-14	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–119（119 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.4 mM [U-13C; U-15N] LC3B, 0.5 mM [U-13C; U-15N] HBx BH3-like motif, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.8 mM 1H LC3B, 0.4 mM [U-13, U-15N] HBx BH3-like motif, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.4 mM [U-15N] LC3B, 0.5 mM [U-15N] HBx BH3-like motif, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-13, U-15N] LC3B, 0.625 mM 1H HBx BH3-like motif, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

49 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MLP3B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–130； UniProt 1–125

Peptide from FYVE and coiled-coil domain-containing protein 1

OrganismNot specified

UniProt Q9BQS8

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 1276–1288	Not recorded	Microtubule-associated proteins 1A/1B light chain 3B × 1 （Q9GZQ8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Potassium thiocyanate, 30%(w/v) Polyethylene glycol monomethyl ether 2000	Resolution 1.53 Å R-free 0.215

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5D94	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 E 1273–1298（26 aa） Chain G 1273–1298（26 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 F 1273–1298（26 aa） Chain H 1273–1298（26 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 E 1273–1298（26 aa） Chain F 1273–1298（26 aa） Chain G 1273–1298（26 aa） Chain H 1273–1298（26 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
7BQI Crystal structure of FYCO1 RUN domain Deposited 2020-03-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–178（178 aa） Fragment：RUN domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% (w/v) PEG 3350, 180mM tri-ammonium citrate	Resolution 1.30 Å R-free 0.240

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

View Construct and Data Evidence

UniProt name	FYCO1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–13； UniProt 1276–1288

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	5d94
Deposition date deposition_date	2015-08-18
Structure title title	Crystal structure of LC3-LIR peptide complex
Keywords keywords	FYCO1, autophagy, LC3, LIR, PROTEIN BINDING-PEPTIDE complex; PROTEIN BINDING/PEPTIDE
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	15.94 Å
Radius of gyration Rg (electron density) rg_electron	14.43 Å
Forward intensity I(0) i0	4458430.00
Molecular weight molecular_weight	15401.0 kDa
Excluded volume excluded_volume	19497 Å³
Envelope volume envelope_volume	21910 Å³
Hydration-shell volume shell_volume	12896 Å³
Envelope diameter envelope_diameter	48.8 Å
Shell Rg shell_rg	20.18 Å
Envelope Rg envelope_rg	14.72 Å
Shape Rg shape_rg	14.40 Å
Total Rg total_rg	15.71 Å
Total atoms total_atoms	1085
Residues n_residues	131
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	50.2 Å
Rg (real space) rg_real	15.83 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	4.4580e+06
I(0) uncertainty (real space) i0_real_error	4.8620e+04
Rg (reciprocal space) rg_reciprocal	15.84 Å
I(0) (reciprocal space) i0_reciprocal	4458000.0000
Solution quality estimate total_estimate	0.8889
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.5 Å
Skewness Skewness skewness	0.095
Kurtosis Kurtosis kurtosis	-0.377
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	823200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.978

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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 3B
Molecular weight formula_weight	15121.5 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	1293

GPLGSMPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVYASQETFGMKLSV

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	Peptide from FYVE and coiled-coil domain-containing protein 1
Molecular weight formula_weight	1494.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DDAVFDIITDEEL

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5d94A00
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	40.724 Å
Unit-cell length b length_b	39.162 Å
Unit-cell length c length_c	42.756 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.530 Å
Low-resolution limit resolution_low	19.580 Å
R factor r_factor	0.1767
R_work r_work	0.1747
R_free r_free	0.2147

fit	/app/data/saxs_computation/d9/5d94/5d94.fit
pddf	/app/data/pr_computation/d9/5d94/5d94.pr.out
profile	/app/data/saxs_computation/d9/5d94/5d94.dat

Crystal structure of LC3-LIR peptide complex

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

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

State in the Current Structure

Other States of the Same Protein in the Database

Peptide from FYVE and coiled-coil 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

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)