SAXSdb — 3wap

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

Autophagy-related protein 13, 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	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 436–447	Fragment：UNP RESIDUES 436-447, 8-125	No other associated polymer	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
2	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 436–447	Fragment：UNP RESIDUES 436-447, 8-125	No other associated polymer	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

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 3WAP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WAN Crystal structure of Atg13 LIR-fused human LC3A_2-121 Deposited 2013-05-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 436–447（12 aa） Fragment：UNP RESIDUES 436-447, 2-121 Chain B 436–447（12 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
3WAO Crystal structure of Atg13 LIR-fused human LC3B_2-119 Deposited 2013-05-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 436–447（12 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 experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 436–447（12 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 experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 436–447（12 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 experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 436–447（12 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
5C50 Crystal structure of the complex of human Atg101-Atg13 HORMA domain Deposited 2015-06-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 12–200（189 aa） Fragment：UNP residues 12-200	Not recorded	BEN BENZAMIDINE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；19% PEG 3350, 0.5 M benzamidine, and 0.2 M lithium citrate	Resolution 1.63 Å R-free 0.195
5XUY Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.275
5XUY Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.275
5XV1 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.51 Å R-free 0.251
5XV1 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.51 Å R-free 0.251
5XV3 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.57 Å R-free 0.283
5XV3 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.57 Å R-free 0.283
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV6 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.46 Å R-free 0.271
6HYN Structure of ATG13 LIR motif bound to GABARAP Deposited 2018-10-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 441–454（14 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M NaCl, 10% PEG 8000, 0.1M Na K phosphate 6.2	Resolution 1.14 Å R-free 0.185
8DO8 Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer Deposited 2022-07-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–197（197 aa）	Not recorded	GOL GLYCEROL × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；273 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 12% PEG8000	Resolution 2.41 Å R-free 0.251
8DO8 Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer Deposited 2022-07-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–197（197 aa）	Not recorded	GOL GLYCEROL × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；273 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 12% PEG8000	Resolution 2.41 Å R-free 0.251
8SOI Structure of human ULK1 complex core (2:1:1 stoichiometry) Deposited 2023-04-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 346–401（56 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8SQZ Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture Deposited 2023-05-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 363–517（155 aa） Chain F 363–517（155 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.85 Å
8SRM Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 334–401（68 aa） Chain F 334–401（68 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.46 Å

13 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ATG13_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–14； UniProt 436–447

Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3C

Homo sapiens

UniProt Q9BXW4

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 8–125	Fragment：UNP RESIDUES 436-447, 8-125	No other associated polymer	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
2	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 8–125	Fragment：UNP RESIDUES 436-447, 8-125	No other associated polymer	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

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 3WAP	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 oligomeric state 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
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 A 8–125（118 aa） Fragment：UNP residues 8-125	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 C 8–125（118 aa） Fragment：UNP residues 8-125	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 E 8–125（118 aa） Fragment：UNP residues 8-125	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 G 8–125（118 aa） Fragment：UNP residues 8-125	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 I 8–125（118 aa） Fragment：UNP residues 8-125	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 K 8–125（118 aa） Fragment：UNP residues 8-125	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 M 8–125（118 aa） Fragment：UNP residues 8-125	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 O 8–125（118 aa） Fragment：UNP residues 8-125	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

4 other PDB entries and 12 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 17–134； UniProt 8–125

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3wap
Deposition date deposition_date	2013-05-06
Structure title title	Crystal structure of Atg13 LIR-fused human LC3C_8-125
Keywords keywords	UBIQUITIN-LIKE FOLD, AUTOPHAGY, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	15.84 Å
Radius of gyration Rg (electron density) rg_electron	14.71 Å
Forward intensity I(0) i0	3846100.00
Molecular weight molecular_weight	14413.0 kDa
Excluded volume excluded_volume	18384 Å³
Envelope volume envelope_volume	21235 Å³
Hydration-shell volume shell_volume	12496 Å³
Envelope diameter envelope_diameter	54.7 Å
Shell Rg shell_rg	20.17 Å
Envelope Rg envelope_rg	15.11 Å
Shape Rg shape_rg	14.70 Å
Total Rg total_rg	15.96 Å
Total atoms total_atoms	1014
Residues n_residues	124
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	54.3 Å
Rg (real space) rg_real	15.77 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	3.8460e+06
I(0) uncertainty (real space) i0_real_error	4.4660e+04
Rg (reciprocal space) rg_reciprocal	15.78 Å
I(0) (reciprocal space) i0_reciprocal	3846000.0000
Solution quality estimate total_estimate	0.7802
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.8 Å
Skewness Skewness skewness	0.222
Kurtosis Kurtosis kurtosis	-0.192
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	800500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3wapa_
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 (1 domains)

Domain ID domain_id	3wapA00
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	61.730 Å
Unit-cell length b length_b	61.730 Å
Unit-cell length c length_c	95.881 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	53.460 Å
R factor r_factor	0.2104
R_work r_work	0.2074
R_free r_free	0.2732

Description description	Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3C
Molecular weight formula_weight	15401.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1014

Crystal structure of Atg13 LIR-fused human LC3C_8-125

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

Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3C

State in the Current Structure

Other States of the Same Protein in the Database

Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3C

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/wa/3wap/3wap.fit
pddf	/app/data/pr_computation/wa/3wap/3wap.pr.out
profile	/app/data/saxs_computation/wa/3wap/3wap.dat