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6dst

Recombinant melittin

Method: SOLUTION NMR Dmax: 41.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Melittin

Apis mellifera

UniProt P01501

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 44–69 Fragment：residues 44-69 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR measurement conditions：pH 7；285 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition：0.05 mM [U-95% 13C; U-95% 15N] melittin, 10 % v/v [U-2H] glycerol, 10 mM potassium phosphate buffer, trifluoroethanol/water | trifluoroethanol/water NMR sample composition：0.050 mM [U-95% 13C; U-95% 15N] Melittin, 10 mM potassium phosphate buffer, trifluoroethanol/water | trifluoroethanol/water 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 6DST Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BH1 STRUCTURAL STUDIES OF D-PRO MELITTIN, NMR, 20 STRUCTURES Deposited 1998-06-11 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–69（26 aa）
Mutation：PRO 14 REPLACED WITH D-PRO Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.2；277 K；Ionic strength (raw mmCIF value) 2mM；Pressure 1
NMR sample composition METHANOL
Resolution not provided
2MLT MELITTIN Deposited 1990-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 44–69（26 aa）
Chain B 44–69（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
2MW6 Structure of the bee venom toxin melittin with [(C5H5)Ru]+ fragment attached to the tryptophan residue Deposited 2014-10-28 Different mutation/modification Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–69（26 aa） Fragment：residues 44-69
Non-standard monomer：Yes (specific site not provided by mmCIF) 3UQ [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,4a,8a-eta)-naphthalene]ruthenium(1+) × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Pressure 1
NMR sample composition 6 mM Ru-melittin-1, CD3OH | CD3OH
Resolution not provided
3QRX Chlamydomonas reinhardtii centrin bound to melittin Deposited 2011-02-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 44–69（26 aa） Fragment：residues 44-69
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2 L of the Crcen-MLT (1:1.5 molar ratio, 10mg/mL total) solution with 2 L of a precipitant solution containing 50 mM HEPES, pH 7.5, 0.2 M KCl, and 40% v/v pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.341
3QRX Chlamydomonas reinhardtii centrin bound to melittin Deposited 2011-02-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 44–69（26 aa） Fragment：residues 44-69
Not recorded CA CALCIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2 L of the Crcen-MLT (1:1.5 molar ratio, 10mg/mL total) solution with 2 L of a precipitant solution containing 50 mM HEPES, pH 7.5, 0.2 M KCl, and 40% v/v pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.341
6O4M Racemic melittin Deposited 2019-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain C 44–69（26 aa） Fragment：residues 44-69
Chain D 44–69（26 aa） Fragment：residues 44-69
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.05 M ammonium sulfate, 0.1 M BIS-TRIS pH = 6.5, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)
Resolution 1.27 Å R-free 0.235
6O4M Racemic melittin Deposited 2019-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 44–69（26 aa） Fragment：residues 44-69
Chain B 44–69（26 aa） Fragment：residues 44-69
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.05 M ammonium sulfate, 0.1 M BIS-TRIS pH = 6.5, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)
Resolution 1.27 Å R-free 0.235
8AHS Crystal structure of human Ca2+/Calmodulin in complex with melittin Deposited 2022-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 44–69（26 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；0.2M NaCl, 22w/v% PEG3350, 0.1M Bis-Tris, pH 5.4
Resolution 2.48 Å R-free 0.270
8AHT Crystal structure of Plasmodium falciparum Ca2+/Calmodulin in complex with melittin Deposited 2022-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: dimeric
Chain F 44–69（26 aa）
Chain G 44–69（26 aa）
Chain H 44–69（26 aa）
Chain I 44–69（26 aa）
Not recorded CA CALCIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.25M NaCl, 30w/v% PEG3350, 0.1M Bis-Tris buffer, pH 6.0
Resolution 2.20 Å R-free 0.266

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MEL_APIME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–26； UniProt 44–69

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 6dst

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6dst
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6dst
Deposition date deposition_date2018-06-14
Structure title titleRecombinant melittin
Keywords keywordsHemolytic, Antibacterial, Alpha-helical peptide, Bee venom, TOXIN; TOXIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier10.70 Å
Radius of gyration Rg (electron density) rg_electron11.73 Å
Forward intensity I(0) i035043000.00
Molecular weight molecular_weight56711.0 kDa
Excluded volume excluded_volume74554 ų
Envelope volume envelope_volume7076 ų
Hydration-shell volume shell_volume5526 ų
Envelope diameter envelope_diameter43.1 Å
Shell Rg shell_rg16.38 Å
Envelope Rg envelope_rg13.13 Å
Shape Rg shape_rg11.66 Å
Total Rg total_rg12.20 Å
Total atoms total_atoms8620
Residues n_residues520
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 dmax41.9 Å
Rg (real space) rg_real11.00 Å
Rg uncertainty (real space) rg_real_error0.55 Å
I(0) (real space) i0_real3.5040e+07
I(0) uncertainty (real space) i0_real_error3.9320e+05
Rg (reciprocal space) rg_reciprocal10.99 Å
I(0) (reciprocal space) i0_reciprocal35040000.0000
Solution quality estimate total_estimate0.5484
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary5.3 Å
Skewness Skewness skewness0.493
Kurtosis Kurtosis kurtosis-0.852
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2086.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.042; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.002; 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 (2)

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9. Files and Curves (10)