5y2z

Crystal structure of human LGI1 EPTP-ADAM22 complex

Method: X-RAY DIFFRACTION

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

Disintegrin and metalloproteinase domain-containing protein 22

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 2	Leucine-rich glioma-inactivated protein 1 × 1 （O95970） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CALCIUM ION × 4 water × 2	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 2	Leucine-rich glioma-inactivated protein 1 × 1 （O95970） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 water × 2	Consistent with protein count
3	Other combination	Heteromer	Protein 2 其他Polymer 2	Leucine-rich glioma-inactivated protein 1 × 1 （O95970） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 water × 2	Consistent with protein count
4	Other combination	Heteromer	Protein 2 其他Polymer 1	Leucine-rich glioma-inactivated protein 1 × 1 （O95970） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CALCIUM ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
5	Other combination	Heteromer	Protein 2 其他Polymer 2	Leucine-rich glioma-inactivated protein 1 × 1 （O95970） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 water × 2	Consistent with protein count
6	Other combination	Heteromer	Protein 2 其他Polymer 1	Leucine-rich glioma-inactivated protein 1 × 1 （O95970） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ADA22_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–497； UniProt 233–729 Author chain C； PDBConstruct 1–497； UniProt 233–729 Author chain E； PDBConstruct 1–497； UniProt 233–729 Author chain G； PDBConstruct 1–497； UniProt 233–729 Author chain I； PDBConstruct 1–497； UniProt 233–729 Author chain K； PDBConstruct 1–497； UniProt 233–729

Leucine-rich glioma-inactivated protein 1

Homo sapiens

UniProt O95970

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 2	Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CALCIUM ION × 4 water × 2	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 2	Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 water × 2	Consistent with protein count
3	Other combination	Heteromer	Protein 2 其他Polymer 2	Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 water × 2	Consistent with protein count
4	Other combination	Heteromer	Protein 2 其他Polymer 1	Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CALCIUM ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
5	Other combination	Heteromer	Protein 2 其他Polymer 2	Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 water × 2	Consistent with protein count
6	Other combination	Heteromer	Protein 2 其他Polymer 1	Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LGI1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–340； UniProt 224–557 Author chain D； PDBConstruct 7–340； UniProt 224–557 Author chain F； PDBConstruct 7–340； UniProt 224–557 Author chain H； PDBConstruct 7–340； UniProt 224–557 Author chain J； PDBConstruct 7–340； UniProt 224–557 Author chain L； PDBConstruct 7–340； UniProt 224–557

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	5y2z
Deposition date deposition_date	2017-07-27
Structure title title	Crystal structure of human LGI1 EPTP-ADAM22 complex
Keywords keywords	epilepsy, synapse, ADAM, EPTP, WD40, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5y2z__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5y2z__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5y2z__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.55 Å
Rg (electron density)	31.94 Å
Total Rg	32.52 Å
Atom count	6339
Residues	795
Excluded volume	112530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5y2z__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5y2z__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5y2z__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5y2z__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5y2z__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5y2z__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Disintegrin and metalloproteinase domain-containing protein 22
Molecular weight formula_weight	55761.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	39417

NVEEETKYIELMIVNDHLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMETWATDNKFAISENPLITLREFMKYRRDFIKEKSDAVHLFSGSQFESSRSGAAYIGGICSLLKGGGVNEFGKTDLMAVTLAQSLAHNIGIISDKRKLASGECKCEDTWSGCIMGDTGYYLPKKFTQCNIEEYHDFLNSGGGACLFNKPSKLLDPPECGNGFIETGEECDCGTPAECVLEGAECCKKCTLTQDSQCSDGLCCKKCKFQPMGTVCREAVNDCDIRETCSGNSSQCAPNIHKMDGYSCDGVQGICFGGRCKTRDRQCKYIWGQKVTASDKYCYEKLNIEGTEKGNCGKDKDTWIQCNKRDVLCGYLLCTNIGNIPRLGELDGEITSTLVVQQGRTLNCSGGHVKLEEDVDLGYVEDGTPCGPQMMCLEHRCLPVASFNFSTCLSSKEGTICSGNGVCSNELKCVCNRHWIGSDCNTYFPHNDDAKTGITLSGKHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Mammalia

Entity 2 Entity 2 polymer

Description description	Leucine-rich glioma-inactivated protein 1
Molecular weight formula_weight	40378.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

DAAQPATEFAKSQDLPYQSLSIDTFSYLNDEYVVIAQPFTGKCIFLEWDHVEKTFRNYDNITGTSTVVCKPIVIETQLYVIVAQLFGGSHIYKRDSFANKFIKIQDIEILKIRKPNDIETFKIENNWYFVVADSSKAGFTTIYKWNGNGFYSHQSLHAWYRDTDVEYLEIVRTPQTLRTPHLILSSSSQRPVIYQWNKATQLFTNQTDIPNMEDVYAVKHFSVKGDVYICLTRFIGDSKVMKWGGSSFQDIQRMPSRGSMVFQPLQINNYQYAILGSDYSFTQVYNWDAEKAKFVKFQELNVQAPRSFTHVSINKRNFLFASSFKGNTQIYKHVIVDLSAKHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Mammalia

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 4 Entity 4 branched

Description description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	732.7 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 6 Entity 6 branched

Description description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	367.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	man
Copy count entity_count	24

Entity 8 Entity 8 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	914

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	5y2zA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	5y2zA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	70 — Echistatin
Homologous superfamily homologous superfamily	10 — Disintegrin domain

Domain ID domain_id	5y2zC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	5y2zC02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	70 — Echistatin
Homologous superfamily homologous superfamily	10 — Disintegrin domain

Domain ID domain_id	5y2zE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	5y2zE02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	70 — Echistatin
Homologous superfamily homologous superfamily	10 — Disintegrin domain

Domain ID domain_id	5y2zG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	5y2zG02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	70 — Echistatin
Homologous superfamily homologous superfamily	10 — Disintegrin domain

Domain ID domain_id	5y2zI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	5y2zI02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	70 — Echistatin
Homologous superfamily homologous superfamily	10 — Disintegrin domain

Domain ID domain_id	5y2zK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	5y2zK02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	70 — Echistatin
Homologous superfamily homologous superfamily	10 — Disintegrin domain

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Unit-cell length a length_a	83.579 Å
Unit-cell length b length_b	83.608 Å
Unit-cell length c length_c	293.543 Å
Unit-cell angle α angle_alpha	86.40 °
Unit-cell angle β angle_beta	88.17 °
Unit-cell angle γ angle_gamma	59.95 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.670 Å
Low-resolution limit resolution_low	48.827 Å
R factor r_factor	0.2460
R_work r_work	0.2442
R_free r_free	0.2792

Crystal structure of human LGI1 EPTP-ADAM22 complex

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

Disintegrin and metalloproteinase domain-containing protein 22

State in the Current Structure

Other States of the Same Protein in the Database

Leucine-rich glioma-inactivated protein 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5y2z__assembly_3__model_1

5y2z__assembly_3__model_1 | I(q)

5y2z__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of human LGI1 EPTP-ADAM22 complex

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

Disintegrin and metalloproteinase domain-containing protein 22

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Leucine-rich glioma-inactivated protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5y2z__assembly_3__model_1

5y2z__assembly_3__model_1 | I(q)

5y2z__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)