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2mw6

Structure of the bee venom toxin melittin with [(C5H5)Ru]+ fragment attached to the tryptophan residue

Method: SOLUTION NMR Dmax: 38.9 Å Quality: SUSPICIOUS
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Melittin

OrganismNot specified

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 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

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 2MW6 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 ligand/ion 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
3QRX Chlamydomonas reinhardtii centrin bound to melittin Deposited 2011-02-18 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 × 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 mutation/modification 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
6DST Recombinant melittin Deposited 2018-06-14 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
Not recorded No recorded non-water small molecule 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
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 mutation/modification 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 2mw6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2mw6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2mw6
Deposition date deposition_date2014-10-28
Structure title titleStructure of the bee venom toxin melittin with [(C5H5)Ru]+ fragment attached to the tryptophan residue
Keywords keywordstoxin; 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_guinier11.29 Å
Radius of gyration Rg (electron density) rg_electron11.91 Å
Forward intensity I(0) i011503300.00
Molecular weight molecular_weight30177.0 kDa
Excluded volume excluded_volume38894 ų
Envelope volume envelope_volume6159 ų
Hydration-shell volume shell_volume5117 ų
Envelope diameter envelope_diameter42.1 Å
Shell Rg shell_rg15.69 Å
Envelope Rg envelope_rg12.69 Å
Shape Rg shape_rg11.91 Å
Total Rg total_rg12.13 Å
Total atoms total_atoms4470
Residues n_residues260
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 dmax38.9 Å
Rg (real space) rg_real11.57 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real1.1500e+07
I(0) uncertainty (real space) i0_real_error1.1760e+05
Rg (reciprocal space) rg_reciprocal11.56 Å
I(0) (reciprocal space) i0_reciprocal11500000.0000
Solution quality estimate total_estimate0.4195
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary10.3 Å
Skewness Skewness skewness0.469
Kurtosis Kurtosis kurtosis-0.791
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3076.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.202; Stabil: 0.998; Sysdev: 0.256; Positv: 1.000; Valcen: 0.077; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)