SAXSdb — 5y39

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

Ragulator complex protein LAMTOR1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （O43504） water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （O43504） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTOR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–70； UniProt 76–145 Author chain F； PDBConstruct 1–70； UniProt 76–145

Ragulator complex protein LAMTOR2

Homo sapiens

UniProt Q9Y2Q5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （O43504） water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （O43504） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTOR2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–125； UniProt 1–125 Author chain G； PDBConstruct 1–125； UniProt 1–125

Ragulator complex protein LAMTOR3

Homo sapiens

UniProt Q9UHA4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （O43504） water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （O43504） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTOR3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–124； UniProt 1–124 Author chain H； PDBConstruct 1–124； UniProt 1–124

Ragulator complex protein LAMTOR4

Homo sapiens

UniProt Q0VGL1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR5 × 1 （O43504） water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR5 × 1 （O43504） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTOR4_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 3–101； UniProt 1–99 Author chain I； PDBConstruct 3–101； UniProt 1–99

Ragulator complex protein LAMTOR5

Homo sapiens

UniProt O43504

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTOR5_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–90； UniProt 1–90 Author chain J； PDBConstruct 1–90； UniProt 1–90

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	5y39
Deposition date deposition_date	2017-07-28
Structure title title	Crystal structure of Ragulator complex (p18 76-145)
Keywords keywords	Ragulator complex, LAMTOR, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

5y39__assembly_1__model_1

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

Download this curve (.dat)

5y39__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5y39__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.64 Å
Rg (electron density)	24.48 Å
Total Rg	25.32 Å
Atom count	3760
Residues	493
Excluded volume	67130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5y39__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5y39__assembly_2__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	Ragulator complex protein LAMTOR1
Molecular weight formula_weight	7966.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	6808

MEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQ

Source Source

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

Entity 2 Entity 2 polymer

Description description	Ragulator complex protein LAMTOR2
Molecular weight formula_weight	13517.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,G

MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLTQVAAS

Source Source

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

Entity 3 Entity 3 polymer

Description description	Ragulator complex protein LAMTOR3
Molecular weight formula_weight	13637.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H

MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQVVEVS

Source Source

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

Entity 4 Entity 4 polymer

Description description	Ragulator complex protein LAMTOR4
Molecular weight formula_weight	10941.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I

MGMTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMNVPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Source Source

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

Entity 5 Entity 5 polymer

Description description	Ragulator complex protein LAMTOR5
Molecular weight formula_weight	9535.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,J

MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMA

Source Source

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5y39b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.7 — Roadblock/LC7 domain
Family Family family	d.110.7.1 — Roadblock/LC7 domain

Domain ID domain_id	d5y39c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.7 — Roadblock/LC7 domain
Family Family family	d.110.7.1 — Roadblock/LC7 domain

Domain ID domain_id	d5y39g_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.7 — Roadblock/LC7 domain
Family Family family	d.110.7.1 — Roadblock/LC7 domain

Domain ID domain_id	d5y39h_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.7 — Roadblock/LC7 domain
Family Family family	d.110.7.1 — Roadblock/LC7 domain

CATH v4.4 (6 domains)

Domain ID domain_id	5y39B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	5y39C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	5y39E00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	5y39G00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	5y39H00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	5y39J00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

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Unit-cell length a length_a	110.659 Å
Unit-cell length b length_b	117.854 Å
Unit-cell length c length_c	157.805 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	50.010 Å
R factor r_factor	0.2180
R_work r_work	0.2155
R_free r_free	0.2626

Crystal structure of Ragulator complex (p18 76-145)

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

Ragulator complex protein LAMTOR1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ragulator complex protein LAMTOR2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ragulator complex protein LAMTOR3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ragulator complex protein LAMTOR4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ragulator complex protein LAMTOR5

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

5y39__assembly_1__model_1

5y39__assembly_1__model_1 | I(q)

5y39__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)