SAXSdb — 2naj

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

Tau-theraphotoxin-Hs1a

OrganismNot specified

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 43–75	Fragment：K2 domain, UNP residues 43-75	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 4；298 K；Pressure ambient NMR sample composition：1 mM K2-1, 90% H2O/10% D2O \| 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 2NAJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N9Z Solution structure of K1 lobe of double-knot toxin Deposited 2015-12-16	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–42（42 aa） Fragment：K1 domain, UNP residues 1-42	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；298 K；Pressure ambient NMR sample composition 1 mM K1-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5IRX Structure of TRPV1 in complex with DkTx and RTX, determined in lipid nanodisc Deposited 2016-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–75（75 aa） Chain F 1–75（75 aa）	Not recorded	6O8 (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium × 4 6OE (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate × 8 6EU resiniferatoxin × 4 6O9 (2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).	Resolution 2.95 Å
6CUC Solution structure of double knot toxin (DkTx) Deposited 2018-03-25	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–79（79 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 300 uM [U-13C; U-15N] DkTx, 20 mM sodium phosphate, 10 uM DSS, 0.02 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7L2M Cryo-EM structure of DkTx/RTX-bound full-length TRPV1 Deposited 2020-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–75（75 aa） Chain F 1–75（75 aa）	Not recorded	6EU resiniferatoxin × 4 NA SODIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
7L2R Cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-open state Deposited 2020-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–75（75 aa） Chain F 1–75（75 aa）	Not recorded	XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 65I (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate × 4 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7L2T cryo-EM structure of DkTx-bound minimal TRPV1 in partial open state Deposited 2020-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–75（75 aa） Chain F 1–75（75 aa）	Not recorded	XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 NA SODIUM ION × 1 65I (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
7L2U cryo-EM structure of DkTx-bound minimal TRPV1 in open state Deposited 2020-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–75（75 aa） Chain F 1–75（75 aa）	Not recorded	XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 XKP (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate × 4 NA SODIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DKTX_HAPSC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–33； UniProt 43–75

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	2naj
Deposition date deposition_date	2016-01-04
Structure title title	Solution structure of K2 lobe of double-knot toxin
Keywords keywords	trpv1, toxins, tarantula, spider, ICK, double-knot toxin, DkTx, K2, TOXIN; TOXIN
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	8.25 Å
Radius of gyration Rg (electron density) rg_electron	8.95 Å
Forward intensity I(0) i0	86661100.00
Molecular weight molecular_weight	73285.0 kDa
Excluded volume excluded_volume	89535 Å³
Envelope volume envelope_volume	9390 Å³
Hydration-shell volume shell_volume	7653 Å³
Envelope diameter envelope_diameter	35.8 Å
Shell Rg shell_rg	16.08 Å
Envelope Rg envelope_rg	11.38 Å
Shape Rg shape_rg	9.00 Å
Total Rg total_rg	9.06 Å
Total atoms total_atoms	9660
Residues n_residues	660
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	30.6 Å
Rg (real space) rg_real	8.25 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	8.6660e+07
I(0) uncertainty (real space) i0_real_error	9.4580e+05
Rg (reciprocal space) rg_reciprocal	8.25 Å
I(0) (reciprocal space) i0_reciprocal	86660000.0000
Solution quality estimate total_estimate	0.7369
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	9.7 Å
Skewness Skewness skewness	0.379
Kurtosis Kurtosis kurtosis	0.016
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.571; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.877; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	Tau-theraphotoxin-Hs1a
Molecular weight formula_weight	3686.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9660

fit	/app/data/saxs_computation/na/2naj/2naj.fit
pddf	/app/data/pr_computation/na/2naj/2naj.pr.out
profile	/app/data/saxs_computation/na/2naj/2naj.dat

Solution structure of K2 lobe of double-knot toxin

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

Tau-theraphotoxin-Hs1a

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)