SAXSdb — 1d2l

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

LIPOPROTEIN RECEPTOR RELATED PROTEIN

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 851–893	Fragment：COMPLEMENT-LIKE REPEAT 3 (CR3)	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions：pH 5.5；298 K；Ionic strength (raw mmCIF value) 20 mM NA-D3-ACETATE, 10 mM CACL2；Pressure AMBIENT NMR sample composition：2 MM CR3 U-15N,13C 20 MM NA-D3-ACETATE PH 5.5 10 MM CACL 90% H2O, 10% D2O	Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1D2L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CR8 LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN COMPLEMENT REPEAT 8 Deposited 1998-12-14	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1059–1100（42 aa） Fragment：COMPLEMENT REPEAT 8	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure 1	Resolution not provided
1J8E Crystal structure of ligand-binding repeat CR7 from LRP Deposited 2001-05-21	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1011–1054（44 aa） Fragment：COMPLEMENT-LIKE REPEAT 7 (CR7), LDL-RECEPTOR CLASS A 7	Mutation：C1G	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.8；292 K；0.02M Na-acetate, 0.1M CaCl2, 0.3M NaCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.85 Å R-free 0.222
2FYJ NMR Solution structure of calcium-loaded LRP double module Deposited 2006-02-08	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 932–1013（82 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Pressure ambient NMR measurement conditions pH 7；298 K；Pressure ambient NMR sample composition 0.5mM [U-99% 15N]-CR56 \| 298 K, pH 7.0, no salt NMR sample composition 0.5mM CR56 \| 298 K, pH 7.0, no salt	Resolution not provided
2FYL Haddock model of the complex between double module of LRP, CR56, and first domain of receptor associated protein, RAP-d1. Deposited 2006-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 932–1013（82 aa） Fragment：CR56	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Pressure ambient NMR sample composition 0.1mM [U-99% 15N]-CR56; 0.1mM RAPd1; H2O/D2O (90:10) \| H2O/D2O (90:10) NMR sample composition 0.5mM [U-99% 15N]-RAPd1; 0.5mM CR56; H2O/D2O (90:10) \| H2O/D2O (90:10) NMR sample composition 0.08 mM [U-99% 15N, U-99% 13C]-CR56; 0.08 mM [U-99% 15N, U-99% 13C]-RAPd1; H2O/D2O (90:10) \| H2O/D2O (90:10)	Resolution not provided
2KNX Solution Structure of complement repeat CR17 from LRP-1 Deposited 2009-09-07	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2770–2817（48 aa） Fragment：residues 2770-2817	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7.45；307 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions pH 7.45；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition 150 mM sodium chloride, 20 mM [U-99% 2H] HEPES, 0.7 mM [U-99% 13C; U-99% 15N] protein, 5 mM CALCIUM ION, 3 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KNY Fusion construct of CR17 from LRP-1 and ApoE residues 130-149 Deposited 2009-09-08	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2770–2817（48 aa） Fragment：Fusion of LRP UNP residues 2770-2817 and Apo-E UNP residues 147-167	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7.45；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions pH 7.45；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 20 mM [U-99% 2H] HEPES-1, 50 mM sodium chloride-2, 3 mM sodium azide-3, 5 mM CALCIUM ION-4, 0.8 mM [U-99% 13C; U-99% 15N] entity_1-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-6, 50 mM sodium chloride-7, 3 mM sodium azide-8, 5 mM CALCIUM ION-9, 0.8 mM [U-99% 13C; U-99% 15N] entity_1-10, 100% D2O \| 100% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-11, 50 mM sodium chloride-12, 3 mM sodium azide-13, 5 mM CALCIUM ION-14, 0.8 mM [U-99% 15N] entity_1-15, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-16, 150 mM sodium chloride-17, 3 mM sodium azide-18, 2 mM [U-99% 2H] EDTA-19, 0.5 mM [U-99% 15N] entity_2-20, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-21, 150 mM sodium chloride-22, 3 mM sodium azide-23, 2 mM [U-99% 2H] EDTA-24, 0.5 mM [U-99% 13C; U-99% 15N] entity_2-25, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LRP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–45； UniProt 851–893

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	1d2l
Deposition date deposition_date	1999-09-24
Structure title title	NMR SOLUTION STRUCTURE OF COMPLEMENT-LIKE REPEAT CR3 FROM THE LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN (LRP). EVIDENCE FOR SPECIFIC BINDING TO THE RECEPTOR BINDING DOMAIN OF HUMAN ALPHA-2 MACROGLOBULIN
Keywords keywords	LIGAND BINDING, CALCIUM BINDING, COMPLEMENT-LIKE REPEAT, RECEPTOR, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	9.57 Å
Radius of gyration Rg (electron density) rg_electron	9.61 Å
Forward intensity I(0) i0	198940000.00
Molecular weight molecular_weight	99308.0 kDa
Excluded volume excluded_volume	115830 Å³
Envelope volume envelope_volume	9965 Å³
Hydration-shell volume shell_volume	7958 Å³
Envelope diameter envelope_diameter	38.1 Å
Shell Rg shell_rg	16.26 Å
Envelope Rg envelope_rg	11.60 Å
Shape Rg shape_rg	9.62 Å
Total Rg total_rg	9.74 Å
Total atoms total_atoms	12620
Residues n_residues	900
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	32.5 Å
Rg (real space) rg_real	9.53 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	1.9890e+08
I(0) uncertainty (real space) i0_real_error	1.7730e+06
Rg (reciprocal space) rg_reciprocal	9.53 Å
I(0) (reciprocal space) i0_reciprocal	198900000.0000
Solution quality estimate total_estimate	0.8805
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	12.8 Å
Skewness Skewness skewness	0.167
Kurtosis Kurtosis kurtosis	-0.370
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23760.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d2la1
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	d1d2la2
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	1d2lA00
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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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	LIPOPROTEIN RECEPTOR RELATED PROTEIN
Molecular weight formula_weight	4952.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	12620

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

NMR SOLUTION STRUCTURE OF COMPLEMENT-LIKE REPEAT CR3 FROM THE LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN (LRP). EVIDENCE FOR SPECIFIC BINDING TO THE RECEPTOR BINDING DOMAIN OF HUMAN ALPHA-2 MACROGLOBULIN

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

LIPOPROTEIN RECEPTOR RELATED PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/d2/1d2l/1d2l.fit
pddf	/app/data/pr_computation/d2/1d2l/1d2l.pr.out
profile	/app/data/saxs_computation/d2/1d2l/1d2l.dat