SAXSdb — 1d7n

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

PROTEIN (WASP VENOM PEPTIDE (MASTOPARAN))

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 1–14	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	SOLUTION NMR NMR measurement conditions：303.15 K；Pressure AMBIENT NMR sample composition：5MM MASTOPARAN SODIUM DODECYL SULFATE- D25; 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 1D7N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7RUL I5R8 Mastoparano is a peptide synthetic, modified of Mastoparano (extracted from wasp venom) Deposited 2021-08-17	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–14（14 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) neutral；Pressure 1 NMR sample composition 2 mM I5R8, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8EP5 Solution NMR structure of a computationally designed mastoparan-like peptide, mastoparan-R1 Deposited 2022-10-05	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–14（14 aa）	Mutation：I1K, N2I, A5R, L9K, A10I 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；Ionic strength (raw mmCIF value) acid；Pressure 1 NMR sample composition 1.5 mM Mastoparan-R1, 75 mM [U-98% 2H] SDS-d25, 0.05 % [U-98% 2H] DSS-d6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8ERU Solution NMR structure of a computationally designed mastoparan-like peptide, mastoparan-R4 Deposited 2022-10-12	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–13（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.98；298 K；Ionic strength (raw mmCIF value) acid；Pressure 1 NMR sample composition 1.5 mM Mastoparan-R4 peptide, 75 mg/L [U-98% 2H] SDS-d25, 0.05 % [U-98% 2H] DSS-d6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MAST_VESLE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–14； UniProt 1–14

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	1d7n
Deposition date deposition_date	1999-10-19
Structure title title	SOLUTION STRUCTURE ANALYSIS OF THE MASTOPARAN WITH DETERGENTS
Keywords keywords	SODIUM DODECYL SULFATE BOUND CONFORMATION, IMMUNE SYSTEM, 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	6.33 Å
Radius of gyration Rg (electron density) rg_electron	7.44 Å
Forward intensity I(0) i0	2101590.00
Molecular weight molecular_weight	14820.0 kDa
Excluded volume excluded_volume	20266 Å³
Envelope volume envelope_volume	3968 Å³
Hydration-shell volume shell_volume	4484 Å³
Envelope diameter envelope_diameter	29.2 Å
Shell Rg shell_rg	12.83 Å
Envelope Rg envelope_rg	8.94 Å
Shape Rg shape_rg	7.36 Å
Total Rg total_rg	8.49 Å
Total atoms total_atoms	2360
Residues n_residues	140
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	29.5 Å
Rg (real space) rg_real	6.56 Å
Rg uncertainty (real space) rg_real_error	0.84 Å
I(0) (real space) i0_real	2.1020e+06
I(0) uncertainty (real space) i0_real_error	2.7830e+04
Rg (reciprocal space) rg_reciprocal	6.56 Å
I(0) (reciprocal space) i0_reciprocal	2102000.0000
Solution quality estimate total_estimate	0.6159
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	4.5 Å
Skewness Skewness skewness	0.696
Kurtosis Kurtosis kurtosis	-0.349
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	444.2000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.012; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.989

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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	d1d7na_
Class class	j — Peptides
Fold Fold fold	j.19 — Insect toxins
Superfamily Superfamily superfamily	j.19.1 — Insect toxins
Family Family family	j.19.1.1 — Mellitin-like toxins

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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	PROTEIN (WASP VENOM PEPTIDE (MASTOPARAN))
Molecular weight formula_weight	1480.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2360

fit	/app/data/saxs_computation/d7/1d7n/1d7n.fit
pddf	/app/data/pr_computation/d7/1d7n/1d7n.pr.out
profile	/app/data/saxs_computation/d7/1d7n/1d7n.dat

SOLUTION STRUCTURE ANALYSIS OF THE MASTOPARAN WITH DETERGENTS

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

PROTEIN (WASP VENOM PEPTIDE (MASTOPARAN))

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)