SAXSdb — 6nih

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

Toll-like receptor 1,Variable lymphocyte receptor B

Eptatretus stoutii

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–475	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic pH7.0, 0.1 M imidazole pH7.5 and 18% PEG1900 MME	Resolution 2.30 Å R-free 0.274
2	Insufficient information Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–475	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic pH7.0, 0.1 M imidazole pH7.5 and 18% PEG1900 MME	Resolution 2.30 Å R-free 0.274

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 6NIH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FYV CRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR1 Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 625–785（161 aa） Fragment：TIR DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；100 mM Tris, 1.2M NaH2PO4/K2HPO4 5 mM DTT, 20% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 21K	Resolution 2.90 Å R-free 0.296
2Z7X Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide Deposited 2007-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 25–476（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 PLM PALMITIC ACID × 1 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2M sodium citrate, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.10 Å R-free 0.270
7NT7 Solution structure of toll like receptor 1 (TLR1) TIR domain Deposited 2021-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 625–786（162 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；308 K；Ionic strength (raw mmCIF value) 50；Pressure AMBIENT NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] TLR1-TIR, 20 mM PIPES, 25 mM sodium chloride, 3 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7NUW Crystal structure of the TIR domain of human TLR1 (crystallised with Zn2+ ions) Deposited 2021-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 625–785（161 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；277 K；170 mM Ammonium acetate, 85 mM Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4,000, 15% v/v glycerol (#9 from HR2-122 Hampton) + Zinc chloride(molar ratio zinc chloride:protein 1:1). Growth at +4 for 3-4 months.	Resolution 1.90 Å R-free 0.245
7NUX Crystal structure of the TIR domain of human TLR1 (crystallised without ZN2+ ions) Deposited 2021-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 625–785（161 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；277 K；170 mM Ammonium acetate, 85 mM Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4,000, 15% v/v glycerol (#9 from HR2-122 Hampton) Growth at +4 for 3-4 months.	Resolution 2.47 Å R-free 0.279

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TLR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–475； UniProt 1–475 Author chain B； PDBConstruct 1–475； UniProt 1–475

Toll-like receptor 1,Variable lymphocyte receptor B

Eptatretus stoutii

UniProt Q2YDZ3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 156–224	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic pH7.0, 0.1 M imidazole pH7.5 and 18% PEG1900 MME	Resolution 2.30 Å R-free 0.274
2	Insufficient information Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 156–224	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic pH7.0, 0.1 M imidazole pH7.5 and 18% PEG1900 MME	Resolution 2.30 Å R-free 0.274

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q2YDZ3_EPTST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 477–545； UniProt 156–224 Author chain B； PDBConstruct 477–545； UniProt 156–224

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	6nih
Deposition date deposition_date	2018-12-27
Structure title title	Crystal structure of human TLR1
Keywords keywords	Toll-like receptors, immune system; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	35.00 Å
Radius of gyration Rg (electron density) rg_electron	33.92 Å
Forward intensity I(0) i0	214350000.00
Molecular weight molecular_weight	120930.0 kDa
Excluded volume excluded_volume	153050 Å³
Envelope volume envelope_volume	205290 Å³
Hydration-shell volume shell_volume	48992 Å³
Envelope diameter envelope_diameter	108.4 Å
Shell Rg shell_rg	42.27 Å
Envelope Rg envelope_rg	32.77 Å
Shape Rg shape_rg	33.90 Å
Total Rg total_rg	34.65 Å
Total atoms total_atoms	17089
Residues n_residues	1039
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	100.0 Å
Rg (real space) rg_real	34.73 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	2.1430e+08
I(0) uncertainty (real space) i0_real_error	3.0570e+06
Rg (reciprocal space) rg_reciprocal	34.90 Å
I(0) (reciprocal space) i0_reciprocal	214400000.0000
Solution quality estimate total_estimate	0.8935
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	51.1 Å
Skewness Skewness skewness	-0.085
Kurtosis Kurtosis kurtosis	-0.617
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	56610000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.804

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Toll-like receptor 1,Variable lymphocyte receptor B
Molecular weight formula_weight	62346.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	17381

MTSIFHFAIIFMLILQIRIQLSEESEFLVDRSKNGLIHVPKDLSQKTTILNISQNYISELWTSDILSLSKLRILIISHNRIQYLDISVFKFNQELEYLDLSHNKLVKISCHPTVNLKHLDLSFNAFDALPICKEFGNMSQLKFLGLSTTHLEKSSVLPIAHLNISKVLLVLGETYGEKEDPEGLQDFNTESLHIVFPTNKEFHFILDVSVKTVANLELSNIKCVLEDNKCSYFLSILAKLQTNPKLSNLTLNNIETTWNSFIRILQLVWHTTVWYFSISNVKLQGQLDFRDFDYSGTSLKALSIHQVVSDVFGFPQSYIYEIFSNMNIKNFTVSGTRMVHMLCPSKISPFLHLDFSNNLLTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNSVSYDEKKGDCSWTKSLLSLNMSSNILTDTIFRCLPPRIKVLDLHSNKIKSIPKQVVKLEALQELNVASNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPT

来源 Source

来源生物 organism	Eptatretus stoutii
通用名 common_name	Pacific hagfish
NCBI Class编号 ncbi_taxonomy_id	7765
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	nat
Copy count entity_count	3

Entity 3 Entity 3 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	627.6 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	216

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8. Citations (1)

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Unit-cell length a length_a	79.028 Å
Unit-cell length b length_b	74.377 Å
Unit-cell length c length_c	106.076 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	46.397 Å
R factor r_factor	0.2449
R_work r_work	0.2435
R_free r_free	0.2736

fit	/app/data/saxs_computation/ni/6nih/6nih.fit
pddf	/app/data/pr_computation/ni/6nih/6nih.pr.out
profile	/app/data/saxs_computation/ni/6nih/6nih.dat

Crystal structure of human TLR1

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

Toll-like receptor 1,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Toll-like receptor 1,Variable lymphocyte receptor B

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)