SAXSdb — 5vok

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

Ragulator complex protein LAMTOR5

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ragulator complex protein LAMTOR4 × 1 （Q0VGL1）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ragulator complex protein LAMTOR4 × 1 （Q0VGL1）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ragulator complex protein LAMTOR4 × 1 （Q0VGL1）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	Ragulator complex protein LAMTOR4 × 2 （Q0VGL1）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 4	Ragulator complex protein LAMTOR4 × 2 （Q0VGL1） water × 2	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 1–91 Author chain C； PDBConstruct 1–91； UniProt 1–91 Author chain E； PDBConstruct 1–91； UniProt 1–91 Author chain G； PDBConstruct 1–91； UniProt 1–91

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 2	Ragulator complex protein LAMTOR5 × 1 （O43504）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ragulator complex protein LAMTOR5 × 1 （O43504）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ragulator complex protein LAMTOR5 × 1 （O43504） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ragulator complex protein LAMTOR5 × 1 （O43504）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	Ragulator complex protein LAMTOR5 × 2 （O43504）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 4	Ragulator complex protein LAMTOR5 × 2 （O43504） water × 2	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–103； UniProt 1–99 Author chain D； PDBConstruct 5–103； UniProt 1–99 Author chain F； PDBConstruct 5–103； UniProt 1–99 Author chain H； PDBConstruct 5–103； UniProt 1–99

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	5vok
Deposition date deposition_date	2017-05-03
Structure title title	Crystal structure of the C7orf59-HBXIP dimer
Keywords keywords	C7orf59, Ragulator, Roadblock, mTOR, 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.

5vok__assembly_1__model_1

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

Download this curve (.dat)

5vok__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vok__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.48 Å
Rg (electron density)	18.49 Å
Total Rg	19.45 Å
Atom count	1365
Residues	183
Excluded volume	24232 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vok__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5vok__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5vok__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5vok__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5vok__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5vok__assembly_6__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	Ragulator complex protein LAMTOR5
Molecular weight formula_weight	9622.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	5252

MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS

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 LAMTOR4
Molecular weight formula_weight	11051.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

GPGSMTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMNVPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5vokA00
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	5vokC00
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	5vokE00
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	5vokG00
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	180.884 Å
Unit-cell length b length_b	64.763 Å
Unit-cell length c length_c	79.231 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	81.846 Å
R factor r_factor	0.2854
R_work r_work	0.2802
R_free r_free	0.3124

Crystal structure of the C7orf59-HBXIP dimer

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

Ragulator complex protein LAMTOR5

State in the Current Structure

Other States of the Same Protein in the Database

Ragulator complex protein LAMTOR4

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

5vok__assembly_1__model_1

5vok__assembly_1__model_1 | I(q)

5vok__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the C7orf59-HBXIP dimer

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5vok__assembly_1__model_1

5vok__assembly_1__model_1 | I(q)

5vok__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)