1n7d

Extracellular domain of the LDL receptor

Method: X-RAY DIFFRACTION

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

Low-density lipoprotein receptor

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 2	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CALCIUM ION × 8 12-TUNGSTOPHOSPHATE × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LDLR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–699； UniProt 22–720

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	1n7d
Deposition date deposition_date	2002-11-13
Structure title title	Extracellular domain of the LDL receptor
Keywords keywords	LDL-Receptor, familial hypercholesterolemia, LDL, cholesterol metabolism, LIPID TRANSPORT; LIPID TRANSPORT
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.

1n7d__assembly_1__model_1

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

Download this curve (.dat)

1n7d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1n7d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.85 Å
Rg (electron density)	34.85 Å
Total Rg	35.56 Å
Atom count	4956
Residues	639
Excluded volume	86112 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1n7d__assembly_1__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	Low-density lipoprotein receptor
Molecular weight formula_weight	77703.6 kDa
Mutation mutation	N494Q, N636Q
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4956

AVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQETCLSVTCKSGDFSCGGRVNRCIPQFWRCDGQVDCDNGSDEQGCPPKTCSQDEFRCHDGKCISRQFVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTCIPQLWACDNDPDCEDGSDEWPQRCRGLYVFQGDSSPCSAFEFHCLSGECIHSSWRCDGGPDCKDKSDEENCAVATCRPDEFQCSDGNCIHGSRQCDREYDCKDMSDEVGCVNVTLCEGPNKFKCHSGECITLDKVCNMARDCRDWSDEPIKECGTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAYLFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTEVASNRIYWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLAVDWIHSNIYWTDSVLGTVSVADTKGVKRKTLFREQGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENIQWPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSDVNLLAENLLSPEDMVLFHQLTQPRGVNWCERTTLSNGGCQYLCLPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

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	8

Entity 5 Entity 5 non-polymer

Description description	12-TUNGSTOPHOSPHATE
Molecular weight formula_weight	2877.0 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1n7da1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.5 — YWTD domain
Family Family family	b.68.5.1 — YWTD domain

Domain ID domain_id	d1n7da2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.1 — EGF-type module

Domain ID domain_id	d1n7da3
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.1 — EGF-type module

Domain ID domain_id	d1n7da4
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.1 — EGF-type module

Domain ID domain_id	d1n7da5
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	d1n7da6
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	d1n7da7
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	d1n7da8
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	d1n7da9
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	d1n7daa
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

CATH v4.4 (10 domains)

Domain ID domain_id	1n7dA01
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

Domain ID domain_id	1n7dA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1220 — Knottins (small inhibitors, toxins, lectins)
Homologous superfamily homologous superfamily	10 — EGF-type module

Domain ID domain_id	1n7dA03
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

Domain ID domain_id	1n7dA04
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

Domain ID domain_id	1n7dA05
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

Domain ID domain_id	1n7dA06
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

Domain ID domain_id	1n7dA07
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	1n7dA08
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	1n7dA09
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	1n7dA10
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

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Unit-cell length a length_a	185.290 Å
Unit-cell length b length_b	185.290 Å
Unit-cell length c length_c	85.186 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.700 Å
Low-resolution limit resolution_low	45.300 Å
R factor r_factor	—
R_work r_work	0.3810
R_free r_free	0.3820

Extracellular domain of the LDL receptor

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

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

1n7d__assembly_1__model_1

1n7d__assembly_1__model_1 | I(q)

1n7d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (2)

Extracellular domain of the LDL receptor

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

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

1n7d__assembly_1__model_1

1n7d__assembly_1__model_1 | I(q)

1n7d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (2)