SAXSdb — 7lk3

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

Gamma-aminobutyric acid receptor-associated protein-like 2

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 1–117	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；294 K；0.15 M KBr, 30% (w/v) PEG monomethyl ether 2000	Resolution 1.90 Å R-free 0.233
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–117	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；294 K；0.15 M KBr, 30% (w/v) PEG monomethyl ether 2000	Resolution 1.90 Å R-free 0.233

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 7LK3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4CO7 Crystal structure of human GATE-16 Deposited 2014-01-27	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100 MM SODIUM PHOSPHATE PH 7.0, 50 MM POTASSIUM CHLORIDE, 10 MM DITHIOTHREITOL	Resolution 2.00 Å R-free 0.212
4CO7 Crystal structure of human GATE-16 Deposited 2014-01-27	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100 MM SODIUM PHOSPHATE PH 7.0, 50 MM POTASSIUM CHLORIDE, 10 MM DITHIOTHREITOL	Resolution 2.00 Å R-free 0.212
6H8C Structure of the human GABARAPL2 protein in complex with the UBA5 LIR motif Deposited 2018-08-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3–116（114 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT NMR sample composition 0.6 mM [U-99% 13C; U-99% 15N] GABARAPL2, 1.0 mM No Ubiquitin-like modifier-activating enzyme 5 (UBA5) LIR motif, 50 mM No sodium phosphate, 100 mM No sodium chloride, 4.6 mM No sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.0 mM No GABARAPL2, 0.6 mM [U-99% 13C; U-99% 15N] Ubiquitin-like modifier-activating enzyme 5 (UBA5) LIR motif, 50 mM No sodium phosphate, 100 mM No sodium chloride, 4.6 mM No sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7YO8 Crystal structure of fission yeast Hfl1 LIR fused to human GABARAPL2 Deposited 2022-08-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–116（116 aa）	Mutation：F28S V29T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；8% PEG 3000, 0.1 M sodium citrate	Resolution 1.80 Å R-free 0.205
8Q6Q Structure of human immunity related GTPase Q in complex with GABARAPL2. Deposited 2023-08-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–117（117 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 % w/v Polyethylene glycol 3,350, 200 mM di-Ammonium hydrogen citrate; pH 5.0	Resolution 1.80 Å R-free 0.222
8Q6Q Structure of human immunity related GTPase Q in complex with GABARAPL2. Deposited 2023-08-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–117（117 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 % w/v Polyethylene glycol 3,350, 200 mM di-Ammonium hydrogen citrate; pH 5.0	Resolution 1.80 Å R-free 0.222

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

View Construct and Data Evidence

UniProt name	GBRL2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–121； UniProt 1–117 Author chain B； PDBConstruct 5–121； UniProt 1–117

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	7lk3
Deposition date deposition_date	2021-02-01
Structure title title	Crystal structure of untwinned human GABARAPL2
Keywords keywords	autophagy, autophagosome, atg8 family, ubiquitin-like, SIGNALING PROTEIN; SIGNALING PROTEIN
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	22.85 Å
Radius of gyration Rg (electron density) rg_electron	22.09 Å
Forward intensity I(0) i0	12291500.00
Molecular weight molecular_weight	27572.0 kDa
Excluded volume excluded_volume	35011 Å³
Envelope volume envelope_volume	42680 Å³
Hydration-shell volume shell_volume	17051 Å³
Envelope diameter envelope_diameter	72.8 Å
Shell Rg shell_rg	27.22 Å
Envelope Rg envelope_rg	21.99 Å
Shape Rg shape_rg	22.07 Å
Total Rg total_rg	22.86 Å
Total atoms total_atoms	1948
Residues n_residues	236
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	73.0 Å
Rg (real space) rg_real	22.95 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.2290e+07
I(0) uncertainty (real space) i0_real_error	1.7290e+05
Rg (reciprocal space) rg_reciprocal	22.93 Å
I(0) (reciprocal space) i0_reciprocal	12290000.0000
Solution quality estimate total_estimate	0.8772
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.379
Kurtosis Kurtosis kurtosis	-0.641
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2526000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.901; Smooth: 0.976

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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	Gamma-aminobutyric acid receptor-associated protein-like 2
Molecular weight formula_weight	14033.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2104

GAMSMKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYSGENTFGF

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	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	148

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d7lk3a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.3 — GABARAP-like

Domain ID domain_id	d7lk3a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d7lk3b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.3 — GABARAP-like

Domain ID domain_id	d7lk3b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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8. Citations (1)

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Unit-cell length a length_a	28.402 Å
Unit-cell length b length_b	58.700 Å
Unit-cell length c length_c	67.997 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	33.650 Å
R factor r_factor	—
R_work r_work	0.1958
R_free r_free	0.2326

fit	/app/data/saxs_computation/lk/7lk3/7lk3.fit
pddf	/app/data/pr_computation/lk/7lk3/7lk3.pr.out
profile	/app/data/saxs_computation/lk/7lk3/7lk3.dat

Crystal structure of untwinned human GABARAPL2

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

Gamma-aminobutyric acid receptor-associated protein-like 2

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