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8eru

Solution NMR structure of a computationally designed mastoparan-like peptide, mastoparan-R4

Method: SOLUTION NMR Dmax: 27.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mastoparan-R4 peptide

OrganismNot specified

UniProt P01514

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 B； UniProt 1–13 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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

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 8ERU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D7N SOLUTION STRUCTURE ANALYSIS OF THE MASTOPARAN WITH DETERGENTS Deposited 1999-10-19 Different construct 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 303.15 K；Pressure AMBIENT
NMR sample composition 5MM MASTOPARAN SODIUM DODECYL SULFATE- D25; 90% H2O, 10% D2O
Resolution not provided
7RUL I5R8 Mastoparano is a peptide synthetic, modified of Mastoparano (extracted from wasp venom) Deposited 2021-08-17 Different construct 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 construct 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

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 B； PDBConstruct 1–14； UniProt 1–13

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.

SAXS scattering curve SAXS Profile

SAXS profile for 8eru

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8eru
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8eru
Deposition date deposition_date2022-10-12
Structure title titleSolution NMR structure of a computationally designed mastoparan-like peptide, mastoparan-R4
Keywords keywordsAntimicrobial Peptide, AMPs, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier6.59 Å
Radius of gyration Rg (electron density) rg_electron7.56 Å
Forward intensity I(0) i02795020.00
Molecular weight molecular_weight16422.0 kDa
Excluded volume excluded_volume22273 ų
Envelope volume envelope_volume3788 ų
Hydration-shell volume shell_volume4347 ų
Envelope diameter envelope_diameter30.2 Å
Shell Rg shell_rg12.74 Å
Envelope Rg envelope_rg8.86 Å
Shape Rg shape_rg7.48 Å
Total Rg total_rg8.51 Å
Total atoms total_atoms2680
Residues n_residues140
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax27.8 Å
Rg (real space) rg_real6.78 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real2.7950e+06
I(0) uncertainty (real space) i0_real_error2.9650e+04
Rg (reciprocal space) rg_reciprocal6.78 Å
I(0) (reciprocal space) i0_reciprocal2795000.0000
Solution quality estimate total_estimate0.6548
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary4.9 Å
Skewness Skewness skewness0.605
Kurtosis Kurtosis kurtosis-0.315
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha543.1000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.209; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.008; Smooth: 0.875
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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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9. Files and Curves (10)