SAXSdb — 5y30

▼

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

Leucine-rich glioma-inactivated protein 1

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 37–223	Fragment：LGI1 LRR domain (UNP RESIDUES 37-223)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；20% PEG 4000, 0.2 M ammonium acetate, 0.1 M tri-sodium citrate (pH 5.5)	Resolution 1.78 Å R-free 0.191

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 5Y30	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 224–557（334 aa） Fragment：UNP RESIDUES 224-557	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)	Resolution 2.67 Å R-free 0.279
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 224–557（334 aa） Fragment：UNP RESIDUES 224-557	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)	Resolution 2.67 Å R-free 0.279
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 224–557（334 aa） Fragment：UNP RESIDUES 224-557	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)	Resolution 2.67 Å R-free 0.279
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 224–557（334 aa） Fragment：UNP RESIDUES 224-557	Not recorded	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)	Resolution 2.67 Å R-free 0.279
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 224–557（334 aa） Fragment：UNP RESIDUES 224-557	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)	Resolution 2.67 Å R-free 0.279
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 224–557（334 aa） Fragment：UNP RESIDUES 224-557	Not recorded	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)	Resolution 2.67 Å R-free 0.279
5Y31 Crystal structure of human LGI1-ADAM22 complex Deposited 2017-07-27	Different construct Different mutation/modification 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 37–557（521 aa） Fragment：UNP RESIDUES 37-557	Mutation：R470A	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)	Resolution 7.12 Å R-free 0.316
5Y31 Crystal structure of human LGI1-ADAM22 complex Deposited 2017-07-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 37–557（521 aa） Fragment：UNP RESIDUES 37-557	Mutation：R470A	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)	Resolution 7.12 Å R-free 0.316
8HPY Crystal structure of human LGI1-ADAM22 complex Deposited 2022-12-13	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 D 39–557（519 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.5M sodium chloride, 0.1M HEPES pH=7.5, 2% (w/v) Benzamidine	Resolution 5.87 Å R-free 0.343
8HPY Crystal structure of human LGI1-ADAM22 complex Deposited 2022-12-13	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 E 39–557（519 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.5M sodium chloride, 0.1M HEPES pH=7.5, 2% (w/v) Benzamidine	Resolution 5.87 Å R-free 0.343
8HQ1 Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2 Deposited 2022-12-13	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 D 39–557（519 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；2M SODIUM CHLORIDE, 0.1M POTASSIUM/SODIUM PHOSPHATE pH=6.2	Resolution 4.17 Å R-free 0.314
8HQ1 Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2 Deposited 2022-12-13	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 E 39–557（519 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；2M SODIUM CHLORIDE, 0.1M POTASSIUM/SODIUM PHOSPHATE pH=6.2	Resolution 4.17 Å R-free 0.314
8HQ1 Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2 Deposited 2022-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 39–557（519 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；2M SODIUM CHLORIDE, 0.1M POTASSIUM/SODIUM PHOSPHATE pH=6.2	Resolution 4.17 Å R-free 0.314
8HQ2 Crystal structure of human ADAM22 in complex with human LGI1 mutant Deposited 2022-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 39–557（519 aa）	Mutation：L88N/F89A/R474Q	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；7.5% PEG 4000, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH=7.5	Resolution 2.93 Å R-free 0.291
8HQ2 Crystal structure of human ADAM22 in complex with human LGI1 mutant Deposited 2022-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 39–557（519 aa）	Mutation：L88N/F89A/R474Q	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；7.5% PEG 4000, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH=7.5	Resolution 2.93 Å R-free 0.291
8Y6B Structure of human LGI1-ADAM22 complex in space group P212121 Deposited 2024-02-02	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 D 39–557（519 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.8M sodium/potassium tartrate, 0.1M Tris pH=7.0, 0.2M lithium sulfate.	Resolution 3.49 Å R-free 0.277
8Y6B Structure of human LGI1-ADAM22 complex in space group P212121 Deposited 2024-02-02	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 F 39–557（519 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.8M sodium/potassium tartrate, 0.1M Tris pH=7.0, 0.2M lithium sulfate.	Resolution 3.49 Å R-free 0.277
8Y6B Structure of human LGI1-ADAM22 complex in space group P212121 Deposited 2024-02-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 39–557（519 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.8M sodium/potassium tartrate, 0.1M Tris pH=7.0, 0.2M lithium sulfate.	Resolution 3.49 Å R-free 0.277
9KZC Cryo-EM structure of the LGI1 LRR-LGI1 EPTP-ADAM22 ECD complex Deposited 2024-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 37–557（521 aa） Fragment：UNP RESIDUES 37-557 Chain D 37–557（521 aa） Fragment：UNP RESIDUES 37-557	Mutation：R470A Mutation：R470A	CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9KZT Cryo-EM structure of the 3:3 LGI1-ADAM22 complex Deposited 2024-12-11	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 B 37–557（521 aa） Fragment：UNP RESIDUES 37-557 Chain D 37–557（521 aa） Fragment：UNP RESIDUES 37-557 Chain F 37–557（521 aa） Fragment：UNP RESIDUES 37-557	Mutation：R470A Mutation：R470A Mutation：R470A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.79 Å

8 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LGI1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–203； UniProt 37–223

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5y30
Deposition date deposition_date	2017-07-27
Structure title title	Crystal structure of LGI1 LRR domain
Keywords keywords	epilepsy, synapse, ADAM, EPTP, WD40, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.25 Å
Radius of gyration Rg (electron density) rg_electron	17.08 Å
Forward intensity I(0) i0	7623300.00
Molecular weight molecular_weight	20419.0 kDa
Excluded volume excluded_volume	25660 Å³
Envelope volume envelope_volume	29611 Å³
Hydration-shell volume shell_volume	15113 Å³
Envelope diameter envelope_diameter	64.8 Å
Shell Rg shell_rg	22.57 Å
Envelope Rg envelope_rg	17.45 Å
Shape Rg shape_rg	17.01 Å
Total Rg total_rg	18.23 Å
Total atoms total_atoms	1436
Residues n_residues	182
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	62.6 Å
Rg (real space) rg_real	18.25 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	7.6230e+06
I(0) uncertainty (real space) i0_real_error	1.0430e+05
Rg (reciprocal space) rg_reciprocal	18.25 Å
I(0) (reciprocal space) i0_reciprocal	7623000.0000
Solution quality estimate total_estimate	0.7831
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.386
Kurtosis Kurtosis kurtosis	-0.104
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	877000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.728; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5y30a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.2 — L domain-like
Family Family family	c.10.2.0 — automated matches

▶

8. Citations (1)

▶

Unit-cell length a length_a	65.252 Å
Unit-cell length b length_b	65.252 Å
Unit-cell length c length_c	109.741 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 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	1.781 Å
Low-resolution limit resolution_low	39.366 Å
R factor r_factor	0.1667
R_work r_work	0.1655
R_free r_free	0.1911

Description description	Leucine-rich glioma-inactivated protein 1
Molecular weight formula_weight	23808.1 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	1560

Crystal structure of LGI1 LRR domain

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

Leucine-rich glioma-inactivated 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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (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	Homo sapiens

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

fit	/app/data/saxs_computation/y3/5y30/5y30.fit
pddf	/app/data/pr_computation/y3/5y30/5y30.pr.out
profile	/app/data/saxs_computation/y3/5y30/5y30.dat