SAXSdb — 7r9z

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

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

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–120	Not recorded	2LZ (5-fluoro-1H-indol-3-yl)acetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Sodium formate, 20% PEG 3350	Resolution 1.72 Å R-free 0.218

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 7R9Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ECI Microtubule-associated protein 1 light chain 3 alpha isoform A (MAP1ALC3) Deposited 2008-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；32 % PEG 4000, 0.1 M NA ACETATE, PH 4.50, 0.2 M AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, CRYOPROTECTION 20% GLYCEROL, TEMPERATURE 298K	Resolution 2.65 Å R-free 0.304
3ECI Microtubule-associated protein 1 light chain 3 alpha isoform A (MAP1ALC3) Deposited 2008-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–121（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；32 % PEG 4000, 0.1 M NA ACETATE, PH 4.50, 0.2 M AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, CRYOPROTECTION 20% GLYCEROL, TEMPERATURE 298K	Resolution 2.65 Å R-free 0.304
3WAL Crystal structure of human LC3A_2-121 Deposited 2013-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–121（120 aa）	Not recorded	MLT D-MALATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.2M Sodium malonate, 20% PEG 3350, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.237
3WAN Crystal structure of Atg13 LIR-fused human LC3A_2-121 Deposited 2013-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–121（120 aa） Fragment：UNP RESIDUES 436-447, 2-121 Chain B 2–121（120 aa） Fragment：UNP RESIDUES 436-447, 2-121	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；12% MPD, 0.1M Sodium chloride, 0.1M Sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.77 Å R-free 0.227
4ZDV Crystal structure of LC3 in complex with FAM134B LIR Deposited 2015-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–120（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8% Tacsimate (Hampton Research) pH 8.0, 20% Poly ethylene glycol 3350	Resolution 1.80 Å R-free 0.223
5CX3 Crystal structure of FYCO1 LIR in complex with LC3A Deposited 2015-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–121（121 aa） Chain C 1–121（121 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；289 K；1.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES sodium	Resolution 2.30 Å R-free 0.244
5CX3 Crystal structure of FYCO1 LIR in complex with LC3A Deposited 2015-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–121（121 aa） Chain D 1–121（121 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；289 K；1.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES sodium	Resolution 2.30 Å R-free 0.244
5CX3 Crystal structure of FYCO1 LIR in complex with LC3A Deposited 2015-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa） Chain B 1–121（121 aa） Chain C 1–121（121 aa） Chain D 1–121（121 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；289 K；1.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES sodium	Resolution 2.30 Å R-free 0.244
5DPR Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121 Deposited 2015-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–121（120 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–121（120 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–121（120 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2–121（120 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
6TBE LC3A in complex with (3R,4S,5R,6R)-5-hydroxy-6-((4-hydroxy-3-(4-hydroxy-3-isopentylbenzamido)-8-methyl-2-oxo-2H-chromen-7-yl)oxy)-3-methoxy-2,2-dimethyltetrahydro-2H-pyran-4-yl carbamate Deposited 2019-11-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–119（116 aa）	Not recorded	NOV NOVOBIOCIN × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M ammoniumnitrat and 20% w/v PEG 3350	Resolution 1.67 Å R-free 0.212
7R9W LC3A in complex with Fragment 1-1 Deposited 2021-06-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Not recorded	JO4 4-phenoxybenzoic acid × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Sodium formate, 20% PEG 3350	Resolution 1.75 Å R-free 0.213
7RA0 LC3A in complex with Fragment 2-10 Deposited 2021-06-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Not recorded	2JI (5-ethyl-2-methyl-1H-indol-3-yl)acetic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Sodium formate, 20% PEG 3350	Resolution 1.36 Å R-free 0.201
8T2L Crystal structure of LC3A in complex with the LIR of NSs4 Deposited 2023-06-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa） Fragment：GS is the remain of the removed expression tag. The N terminus of Nss has been fused with Q9H492 to facilitate the crystalization.	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M Na-citrate, 5% Isopropanol, 0.1M MES buffer PH 6.5	Resolution 2.24 Å R-free 0.276
8T2L Crystal structure of LC3A in complex with the LIR of NSs4 Deposited 2023-06-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–121（121 aa） Fragment：GS is the remain of the removed expression tag. The N terminus of Nss has been fused with Q9H492 to facilitate the crystalization.	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M Na-citrate, 5% Isopropanol, 0.1M MES buffer PH 6.5	Resolution 2.24 Å R-free 0.276
8T35 Crystal structure of K51 acetylated LC3A in complex with the LIR of TP53INP2/DOR Deposited 2023-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG4000, 0.1M Na-citrate pH 5.5	Resolution 1.90 Å R-free 0.259
8T36 Crystal structure of K49 acetylated LC3A in complex with the LIR of TP53INP2/DOR Deposited 2023-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa） Fragment：;GS is the remain of the removed expression tag. TP53INP2 Q8IXH6 peptide is fused to the N- terminal of the Q9H492 to facilitate the crystallization. ;	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG3350, 0.1M Na-citrate, 5% isopropanol, 0.1 M HEPES pH 7.5	Resolution 1.85 Å R-free 0.258
8T4T Crystal structure of LC3A in complex with the LIR of TP53INP2/DOR Deposited 2023-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12.5% PEG3350, 0.2M NH4-citrate, 5% isopropanol, 0.1M MES pH6.5	Resolution 2.36 Å R-free 0.272
8T4T Crystal structure of LC3A in complex with the LIR of TP53INP2/DOR Deposited 2023-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–121（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12.5% PEG3350, 0.2M NH4-citrate, 5% isopropanol, 0.1M MES pH6.5	Resolution 2.36 Å R-free 0.272

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MLP3A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–122； UniProt 1–120

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	7r9z
Deposition date deposition_date	2021-06-29
Structure title title	LC3A in complex with Fragment 2-3
Keywords keywords	mAtg8, autophagy, HYDROLASE; HYDROLASE
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	15.61 Å
Radius of gyration Rg (electron density) rg_electron	14.08 Å
Forward intensity I(0) i0	3753720.00
Molecular weight molecular_weight	13784.0 kDa
Excluded volume excluded_volume	17344 Å³
Envelope volume envelope_volume	19756 Å³
Hydration-shell volume shell_volume	12070 Å³
Envelope diameter envelope_diameter	49.5 Å
Shell Rg shell_rg	19.58 Å
Envelope Rg envelope_rg	14.28 Å
Shape Rg shape_rg	14.07 Å
Total Rg total_rg	15.28 Å
Total atoms total_atoms	971
Residues n_residues	115
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	49.9 Å
Rg (real space) rg_real	15.51 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	3.7540e+06
I(0) uncertainty (real space) i0_real_error	3.8210e+04
Rg (reciprocal space) rg_reciprocal	15.52 Å
I(0) (reciprocal space) i0_reciprocal	3754000.0000
Solution quality estimate total_estimate	0.8920
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.3 Å
Skewness Skewness skewness	0.106
Kurtosis Kurtosis kurtosis	-0.422
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	662800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.979

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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 3A
Molecular weight formula_weight	14290.4 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	1049

GSMPSDRPFKQRRSFADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQETFG

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 non-polymer

Description description	(5-fluoro-1H-indol-3-yl)acetic acid
Molecular weight formula_weight	193.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	69

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8. Citations (1)

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Unit-cell length a length_a	93.463 Å
Unit-cell length b length_b	93.463 Å
Unit-cell length c length_c	32.322 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	tetragonal

Resolution resolution	1.720 Å
Low-resolution limit resolution_low	46.730 Å
R factor r_factor	0.1950
R_work r_work	0.1924
R_free r_free	0.2185

fit	/app/data/saxs_computation/r9/7r9z/7r9z.fit
pddf	/app/data/pr_computation/r9/7r9z/7r9z.pr.out
profile	/app/data/saxs_computation/r9/7r9z/7r9z.dat

LC3A in complex with Fragment 2-3

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

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

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