SAXSdb — 6nig

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

Toll-like receptor 2,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 Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–507 Chain B； UniProt 1–507	Fragment：TLR (UNP residues 1-507) + linker + VLR (UNP residues 181-248)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 KQD (3S,4S,3'S,4'S)-1,1'-(1,4-phenylenedicarbonyl)bis{N~3~,N~4~-bis[(1S,2R)-2-phenylcyclopropyl]pyrrolidine-3,4-dicarboxami de} × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic, pH 7.0, 0.1 M imidazole, pH 7.5, 18% PEG1900 MME	Resolution 2.35 Å R-free 0.236
2	Insufficient information Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–507 Chain D； UniProt 1–507	Fragment：TLR (UNP residues 1-507) + linker + VLR (UNP residues 181-248)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 KQD (3S,4S,3'S,4'S)-1,1'-(1,4-phenylenedicarbonyl)bis{N~3~,N~4~-bis[(1S,2R)-2-phenylcyclopropyl]pyrrolidine-3,4-dicarboxami de} × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic, pH 7.0, 0.1 M imidazole, pH 7.5, 18% PEG1900 MME	Resolution 2.35 Å R-free 0.236

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 6NIG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FYW CRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR2 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 636–784（149 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 6.8；277 K；100 mM cacodylate, 10 % PEG 8000, 20 % DMSO, 200 mM MgCl2, 5 mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.00 Å R-free 0.274
1FYW CRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR2 Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 636–784（149 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 6.8；277 K；100 mM cacodylate, 10 % PEG 8000, 20 % DMSO, 200 mM MgCl2, 5 mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.00 Å R-free 0.274
1FYX CRYSTAL STRUCTURE OF P681H MUTANT OF TIR DOMAIN OF HUMAN TLR2 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 636–784（149 aa） Fragment：TIR DOMAIN	Mutation：P681H 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 6.8；277 K；100 mM cacodylate, 10 % PEG 8000, 20 % DMSO, 200 mM MgCl2, 5 mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.80 Å R-free 0.284
1FYX CRYSTAL STRUCTURE OF P681H MUTANT OF TIR DOMAIN OF HUMAN TLR2 Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 636–784（149 aa） Fragment：TIR DOMAIN	Mutation：P681H 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 6.8；277 K；100 mM cacodylate, 10 % PEG 8000, 20 % DMSO, 200 mM MgCl2, 5 mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.80 Å R-free 0.284
1O77 CRYSTAL STRUCTURE OF THE C713S MUTANT OF THE TIR DOMAIN OF HUMAN TLR2 Deposited 2002-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 639–784（146 aa） Fragment：TIR DOMAIN, RESIDUES 639-784 Chain B 639–784（146 aa） Fragment：TIR DOMAIN, RESIDUES 639-784 Chain C 639–784（146 aa） Fragment：TIR DOMAIN, RESIDUES 639-784 Chain D 639–784（146 aa） Fragment：TIR DOMAIN, RESIDUES 639-784	Mutation：YES Mutation：YES Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；1.4M (NH4)2HPO4, 0.1M MES PH 6.5	Resolution 3.20 Å R-free 0.315
1O77 CRYSTAL STRUCTURE OF THE C713S MUTANT OF THE TIR DOMAIN OF HUMAN TLR2 Deposited 2002-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 639–784（146 aa） Fragment：TIR DOMAIN, RESIDUES 639-784	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；1.4M (NH4)2HPO4, 0.1M MES PH 6.5	Resolution 3.20 Å R-free 0.315
2Z7X Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide Deposited 2007-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 27–508（482 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
2Z80 Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide Deposited 2007-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa） Fragment：TLR2, UNP residues 1-284(human), VLRB.61, UNP residues 136-199(Inshore hagfish)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.1M Tris-HCl pH8.5, 28% PEG2000, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.80 Å R-free 0.254
2Z80 Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide Deposited 2007-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–284（284 aa） Fragment：TLR2, UNP residues 1-284(human), VLRB.61, UNP residues 136-199(Inshore hagfish)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.1M Tris-HCl pH8.5, 28% PEG2000, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 1.80 Å R-free 0.254
8AR0 Solution structure of TLR2 transmembrane and cytoplasmic juxtamembrane regions Deposited 2022-08-15	Different construct Different mutation/modification 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 581–629（49 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；318 K；Ionic strength (raw mmCIF value) 50；Pressure AMBIENT NMR measurement conditions pH 7；318 K；Ionic strength (raw mmCIF value) 235；Pressure AMBIENT NMR sample composition 200 uM [U-13C; U-15N] protein, 23.27 mM DMPC, 5.87 mM DMPG, 78.16 mM DHPC, 20 mM potassium phosphate, 4 mM TCEP, 0.05 % w/v sodium azide, 1 mM TSP, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 188 uM [U-15N] protein, 24.23 mM DMPC, 5.50 mM DMPG, 80.18 mM DHPC, 50 mM potassium phosphate, 4 mM TCEP, 0.05 % w/v sodium azide, 1 mM TSP, 30 mg/mL dGpG, 100 mM potassium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TLR2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–507； UniProt 1–507 Author chain B； PDBConstruct 1–507； UniProt 1–507 Author chain C； PDBConstruct 1–507； UniProt 1–507 Author chain D； PDBConstruct 1–507； UniProt 1–507

Toll-like receptor 2,Variable lymphocyte receptor B

Eptatretus stoutii

UniProt Q2YE02

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 Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 181–248 Chain B； UniProt 181–248	Fragment：TLR (UNP residues 1-507) + linker + VLR (UNP residues 181-248)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 KQD (3S,4S,3'S,4'S)-1,1'-(1,4-phenylenedicarbonyl)bis{N~3~,N~4~-bis[(1S,2R)-2-phenylcyclopropyl]pyrrolidine-3,4-dicarboxami de} × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic, pH 7.0, 0.1 M imidazole, pH 7.5, 18% PEG1900 MME	Resolution 2.35 Å R-free 0.236
2	Insufficient information Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 181–248 Chain D； UniProt 181–248	Fragment：TLR (UNP residues 1-507) + linker + VLR (UNP residues 181-248)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 KQD (3S,4S,3'S,4'S)-1,1'-(1,4-phenylenedicarbonyl)bis{N~3~,N~4~-bis[(1S,2R)-2-phenylcyclopropyl]pyrrolidine-3,4-dicarboxami de} × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic, pH 7.0, 0.1 M imidazole, pH 7.5, 18% PEG1900 MME	Resolution 2.35 Å R-free 0.236

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	Q2YE02_EPTST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 509–576； UniProt 181–248 Author chain B； PDBConstruct 509–576； UniProt 181–248 Author chain C； PDBConstruct 509–576； UniProt 181–248 Author chain D； PDBConstruct 509–576； UniProt 181–248

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	6nig
Deposition date deposition_date	2018-12-27
Structure title title	Crystal structure of the human TLR2-Diprovocim complex
Keywords keywords	Toll-like receptors, innate immune agonist, IMMUNE SYSTEM-AGONIST complex; IMMUNE SYSTEM/AGONIST
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	45.89 Å
Radius of gyration Rg (electron density) rg_electron	45.43 Å
Forward intensity I(0) i0	906044000.00
Molecular weight molecular_weight	254540.0 kDa
Excluded volume excluded_volume	321300 Å³
Envelope volume envelope_volume	451700 Å³
Hydration-shell volume shell_volume	82381 Å³
Envelope diameter envelope_diameter	144.0 Å
Shell Rg shell_rg	50.31 Å
Envelope Rg envelope_rg	44.54 Å
Shape Rg shape_rg	45.44 Å
Total Rg total_rg	45.60 Å
Total atoms total_atoms	35927
Residues n_residues	2186
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	149.1 Å
Rg (real space) rg_real	45.75 Å
Rg uncertainty (real space) rg_real_error	1.50 Å
I(0) (real space) i0_real	9.0600e+08
I(0) uncertainty (real space) i0_real_error	1.6740e+07
Rg (reciprocal space) rg_reciprocal	45.89 Å
I(0) (reciprocal space) i0_reciprocal	906200000.0000
Solution quality estimate total_estimate	0.8835
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	57.0 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.442
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	67980000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.840

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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 2,Variable lymphocyte receptor B
Molecular weight formula_weight	65277.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	35983

MPHTLWMVWVLGVIISLSKEESSNQASLSCDRNGICKGSSGSLNSIPSGLTEAVKSLDLSNNRITYISNSDLQRCVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQNVSHLILHMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKITDESLFQVMKLLNQISGLLELEFDDCTLNGVGNFRASDNDRVIDPGKVETLTIRRLHIPRFYLFYDLSTLYSLTERVKRITVENSKVFLVPCLLSQHLKSLEYLDLSENLMVEEYLKNSACEDAWPSLQTLILRQNHLASLEKTGETLLTLKNLTNIDISKNSFHSMPETCQWPEKMKYLNLSSTRIHSVTGCIPKTLEILDVSNNNLNLFSLNLPQLKELYISRNKLMTLPDASLLPMLLVLKISRNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPT

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	4

Entity 3 Entity 3 non-polymer

Description description	;(3S,4S,3'S,4'S)-1,1'-(1,4-phenylenedicarbonyl)bis{N~3~,N~4~-bis[(1S,2R)-2-phenylcyclopropyl]pyrrolidine-3,4-dicarboxami de} ;
Molecular weight formula_weight	909.1 kDa
Source method src_method	man
Copy count entity_count	4

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	9

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

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8. Citations (1)

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Unit-cell length a length_a	66.098 Å
Unit-cell length b length_b	201.252 Å
Unit-cell length c length_c	109.359 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	37.761 Å
R factor r_factor	0.2105
R_work r_work	0.2098
R_free r_free	0.2361

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

Crystal structure of the human TLR2-Diprovocim complex

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

Toll-like receptor 2,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Toll-like receptor 2,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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)