SAXSdb — 5oyl

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

Glycoprotein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Low-density lipoprotein receptor × 1 （P01130） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CALCIUM ION × 2 GLYCEROL × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B7UCZ5_9RHAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–410； UniProt 17–426

Low-density lipoprotein receptor

Homo sapiens

UniProt P01130

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Glycoprotein × 1 （B7UCZ5） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CALCIUM ION × 2 GLYCEROL × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LDLR_HUMAN
Isoform	P01130-5
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 5–46； UniProt 65–106

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	5oyl
Deposition date deposition_date	2017-09-11
Structure title title	VSV G CR2
Keywords keywords	c, VIRAL PROTEIN; VIRAL 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.

5oyl__assembly_1__model_1

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

Download this curve (.dat)

5oyl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5oyl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.72 Å
Rg (electron density)	25.26 Å
Total Rg	25.90 Å
Atom count	3663
Residues	455
Excluded volume	64777 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5oyl__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	Glycoprotein
Molecular weight formula_weight	46097.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3812

KFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCHASKWVTTCDFRWYGPKYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFINGKCSNYICPTVHNSTTWHSDYKVKGLCDSNLISMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCKHWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPVDLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDWAPYEDVEIGPNGVLRTSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHI

Entity 2 Entity 2 polymer

Description description	Low-density lipoprotein receptor
Molecular weight formula_weight	4853.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GPLGSVTCKSGDFSCGGRVNRCIPQFWRCDGQVDCDNGSDEQGCPP

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 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	149

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5oyla_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamily	e.76.1 — Viral glycoprotein ectodomain-like
Family Family family	e.76.1.2 — Spike glycoprotein-like

Domain ID domain_id	d5oyld1
Class class	g — Small proteins
Fold Fold fold	g.12 — LDL receptor-like module
Superfamily Superfamily superfamily	g.12.1 — LDL receptor-like module
Family Family family	g.12.1.1 — LDL receptor-like module

Domain ID domain_id	d5oyld2
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	5oylD00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	400 — Low-density Lipoprotein Receptor
Homologous superfamily homologous superfamily	10 — Low-density Lipoprotein Receptor

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Unit-cell length a length_a	90.040 Å
Unit-cell length b length_b	90.040 Å
Unit-cell length c length_c	515.780 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	29.979 Å
R factor r_factor	0.1899
R_work r_work	0.1882
R_free r_free	0.2238

VSV G CR2

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

Glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

Low-density lipoprotein receptor

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

5oyl__assembly_1__model_1

5oyl__assembly_1__model_1 | I(q)

5oyl__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

7. Citations (1)

VSV G CR2

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

Glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Low-density lipoprotein receptor

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

5oyl__assembly_1__model_1

5oyl__assembly_1__model_1 | I(q)

5oyl__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

7. Citations (1)