SAXSdb — 5t3m

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

Mu-theraphotoxin-Hs2a

Haplopelma schmidti

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 53–87	Fragment：residues 53-87 Mutation：E1G,E4G,Y33W	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition：400 uM [U-99% 13C; U-99% 15N] [m3]-HwTx-IV, 20 mM sodium acetate, 5 % [U-100% 2H] D2O, 95% H2O/5% D2O \| 95% H2O/5% 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 5T3M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MB6 Three dimensional solution structure of huwentoxin-IV by 2D 1H-NMR Deposited 2002-08-02	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–35（35 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；300 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition 5MM HUWENTOXIN-IV MMOL/L PHOSPHATE BUFFER; 90%H2O, 10%D2O \| 90% H2O/10% D2O	Resolution not provided
2M4X Analysis of the structural and molecular basis of voltage-sensitive sodium channel inhibition by the spider toxin, Huwentoxin-IV (-TRTX-Hh2a). Deposited 2013-02-11	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 53–87（35 aa） Fragment：unp residues 53-87	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；25 K；Pressure ambient NMR sample composition 2 mM HWTX-IV, 20 mM sodium phosphate, 150 uM sodium azide, 100 uM EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2M4Z Analysis of the structural and molecular basis of voltage-sensitive sodium channel inhibition by the spider toxin, Huwentoxin-IV (-TRTX-Hh2a). Deposited 2013-02-12	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 53–87（35 aa） Fragment：unp residues 53-87	Mutation：A82W	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；298 K；Pressure ambient NMR sample composition 2 mM entity, 20 mM sodium phosphate, 150 uM sodium azide, 100 uM [U-2H] EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2M50 Analysis of the structural and molecular basis of voltage-sensitive sodium channel inhibition by the spider toxin, Huwentoxin-IV (-TRTX-Hh2a). Deposited 2013-02-12	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 53–87（35 aa） Fragment：unp residues 53-87	Mutation：A82K	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；298 K；Pressure ambient NMR sample composition 2 mM entity, 20 mM sodium phosphate, 150 uM sodium azide, 100 uM [U-99% 2H] EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5TLR Solution NMR structure of gHwTx-IV Deposited 2016-10-11	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–87（34 aa） Fragment：UNP residues 54-87	Mutation：E56G, Y58W, F85W Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；298 K；Pressure ambient NMR measurement conditions pH 4；298 K；Pressure ambient NMR measurement conditions pH 4；283 K；Pressure ambient NMR sample composition 90 % H2O, 10 % D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 100 % D2O, 100% D2O \| 100% D2O	Resolution not provided
6W6O NaChBac-Nav1.7VSDII chimera and HWTX-IV complex Deposited 2020-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain C 53–87（35 aa） Fragment：UNP residues 53-87 Chain E 53–87（35 aa） Fragment：UNP residues 53-87 Chain G 53–87（35 aa） Fragment：UNP residues 53-87 Chain I 53–87（35 aa） Fragment：UNP residues 53-87	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 10 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 5 seconds before plunging	Resolution 3.20 Å
7K48 Structure of NavAb/Nav1.7-VS2A chimera trapped in the resting state by tarantula toxin m3-Huwentoxin-IV Deposited 2020-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain E 53–87（35 aa） Chain F 53–87（35 aa） Chain G 53–87（35 aa） Chain H 53–87（35 aa）	Mutation：E1G, E4G, Y33W Mutation：E1G, E4G, Y33W Mutation：E1G, E4G, Y33W Mutation：E1G, E4G, Y33W	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 2.5-4.0 seconds before plunging	Resolution 3.60 Å

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

View Construct and Data Evidence

UniProt name	TXH4_HAPSC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–35； UniProt 53–87

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	5t3m
Deposition date deposition_date	2016-08-25
Structure title title	Solution structure of a triple mutant of HwTx-IV - a potent blocker of Nav1.7
Keywords keywords	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	8.16 Å
Radius of gyration Rg (electron density) rg_electron	8.82 Å
Forward intensity I(0) i0	99894800.00
Molecular weight molecular_weight	79636.0 kDa
Excluded volume excluded_volume	98173 Å³
Envelope volume envelope_volume	7108 Å³
Hydration-shell volume shell_volume	6519 Å³
Envelope diameter envelope_diameter	32.2 Å
Shell Rg shell_rg	14.79 Å
Envelope Rg envelope_rg	10.26 Å
Shape Rg shape_rg	8.82 Å
Total Rg total_rg	8.98 Å
Total atoms total_atoms	10960
Residues n_residues	700
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	26.5 Å
Rg (real space) rg_real	8.12 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	9.9890e+07
I(0) uncertainty (real space) i0_real_error	9.6790e+05
Rg (reciprocal space) rg_reciprocal	8.12 Å
I(0) (reciprocal space) i0_reciprocal	99890000.0000
Solution quality estimate total_estimate	0.6793
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	10.1 Å
Skewness Skewness skewness	0.097
Kurtosis Kurtosis kurtosis	-0.612
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10840.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.996; 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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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5t3ma_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.6 — omega toxin-like
Family Family family	g.3.6.2 — Spider toxins

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8. Citations (1)

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Description description	Mu-theraphotoxin-Hs2a
Molecular weight formula_weight	3999.8 kDa
Mutation mutation	E1G,E4G,Y33W
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10960

来源生物 organism	Haplopelma schmidti
通用名 common_name	Chinese bird spider
NCBI Class编号 ncbi_taxonomy_id	29017
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/t3/5t3m/5t3m.fit
pddf	/app/data/pr_computation/t3/5t3m/5t3m.pr.out
profile	/app/data/saxs_computation/t3/5t3m/5t3m.dat

Solution structure of a triple mutant of HwTx-IV - a potent blocker of Nav1.7

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

Mu-theraphotoxin-Hs2a

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

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)