SAXSdb — 5yip

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

Gamma-aminobutyric acid receptor-associated protein-like 1

Mus musculus

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 1–117	Not recorded	Ankyrin-3 × 1 （O70511） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.6；289 K；35% w/v Pentaerythritol ethoxylate 797 (15/4 EO/OH), 0.2 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6)	Resolution 1.85 Å R-free 0.222

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 5YIP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7CDB Structure of GABARAPL1 in complex with GABA(A) receptor gamma 2 Deposited 2020-06-19	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 1–117（117 aa）	Not recorded	CIT CITRIC ACID × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；289 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate pH 5.6, and 30% PEG 4000	Resolution 1.95 Å R-free 0.232
7CDB Structure of GABARAPL1 in complex with GABA(A) receptor gamma 2 Deposited 2020-06-19	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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；289 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate pH 5.6, and 30% PEG 4000	Resolution 1.95 Å R-free 0.232

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

View Construct and Data Evidence

UniProt name	GBRL1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–123； UniProt 1–117

Ankyrin-3

Rattus norvegicus

UniProt O70511

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 1985–2010	Fragment：UNP RESIDUES 1985-2010	Gamma-aminobutyric acid receptor-associated protein-like 1 × 1 （Q8R3R8） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.6；289 K；35% w/v Pentaerythritol ethoxylate 797 (15/4 EO/OH), 0.2 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6)	Resolution 1.85 Å R-free 0.222

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 5YIP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YIQ Crystal structure of AnkG LIR/LC3B complex Deposited 2017-10-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1985–2010（26 aa） Fragment：UNP RESIDUES 1985-2010	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；289 K；10% v/v 2-propanol, 0.2 M zinc acetate, 0.1 M MES buffer (pH 6.5)	Resolution 2.60 Å R-free 0.259
6A9X Crystal Structure of AnkG/GABARAP Complex Deposited 2018-07-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1987–2010（24 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；289 K；2.0 M ammonium citrate tribasic, 0.1 M BIS-TRIS propane buffer	Resolution 2.20 Å R-free 0.249
6M3P Crystal structure of AnkG/beta2-spectrin complex Deposited 2020-03-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 975–1465（491 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5	Resolution 3.31 Å R-free 0.295
6M3P Crystal structure of AnkG/beta2-spectrin complex Deposited 2020-03-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 975–1465（491 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5	Resolution 3.31 Å R-free 0.295
6M3R Crystal structure of AnkG/beta4-spectrin complex Deposited 2020-03-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 975–1465（491 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；0.8 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5 and 0.5% w/v polyethylene glycol monomethyl ether 5,000	Resolution 4.31 Å R-free 0.295
7XCE Crystal structure of Ankyrin G in complex with neurofascin Deposited 2022-03-24	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 275–500（226 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289.2 K；0.1 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 17% w/v polyethylene glycol 10000	Resolution 2.50 Å R-free 0.233

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

View Construct and Data Evidence

UniProt name	ANK3_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–26； UniProt 1985–2010

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	5yip
Deposition date deposition_date	2017-10-06
Structure title title	Crystal Structure of AnkG LIR/GABARAPL1 complex
Keywords keywords	Autophagy, 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	16.16 Å
Radius of gyration Rg (electron density) rg_electron	14.68 Å
Forward intensity I(0) i0	5199620.00
Molecular weight molecular_weight	16556.0 kDa
Excluded volume excluded_volume	20749 Å³
Envelope volume envelope_volume	23646 Å³
Hydration-shell volume shell_volume	13574 Å³
Envelope diameter envelope_diameter	50.0 Å
Shell Rg shell_rg	20.62 Å
Envelope Rg envelope_rg	15.00 Å
Shape Rg shape_rg	14.66 Å
Total Rg total_rg	15.89 Å
Total atoms total_atoms	1175
Residues n_residues	146
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	51.4 Å
Rg (real space) rg_real	16.03 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	5.2000e+06
I(0) uncertainty (real space) i0_real_error	5.2360e+04
Rg (reciprocal space) rg_reciprocal	16.04 Å
I(0) (reciprocal space) i0_reciprocal	5200000.0000
Solution quality estimate total_estimate	0.8815
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.7 Å
Skewness Skewness skewness	0.084
Kurtosis Kurtosis kurtosis	-0.372
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1273000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.977

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Gamma-aminobutyric acid receptor-associated protein-like 1
Molecular weight formula_weight	14642.7 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	1241

GPGSEFMKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ankyrin-3
Molecular weight formula_weight	2920.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PEDDWTEFSSEEIREARQAAASHAPS

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	63

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5yipa1
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	d5yipa2
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

CATH v4.4 (1 domains)

Domain ID domain_id	5yipA00
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	104.172 Å
Unit-cell length b length_b	104.172 Å
Unit-cell length c length_c	63.901 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	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	30.118 Å
R factor r_factor	0.1832
R_work r_work	0.1813
R_free r_free	0.2222

fit	/app/data/saxs_computation/yi/5yip/5yip.fit
pddf	/app/data/pr_computation/yi/5yip/5yip.pr.out
profile	/app/data/saxs_computation/yi/5yip/5yip.dat

Crystal Structure of AnkG LIR/GABARAPL1 complex

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

Gamma-aminobutyric acid receptor-associated protein-like 1

State in the Current Structure

Other States of the Same Protein in the Database

Ankyrin-3

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)