SAXSdb — 9hvn

▼

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

Magainins

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 83–105	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；35% MPD, 20 mM HEPES, pH 7	Resolution 1.05 Å R-free 0.177
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 83–105	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；35% MPD, 20 mM HEPES, pH 7	Resolution 1.05 Å R-free 0.177

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 9HVN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D9J SOLUTION STRUCTURE OF CECROPIN A(1-8)-MAGAININ 2(1-12) HYBRID PEPTIDE Deposited 1999-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 129–140（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.06；298 K；Pressure 1 NMR sample composition 2MM PEPTIDE; 90MM DPC MICELLES; 90% H2O, 10% D2O NMR sample composition 2MM PEPTIDE; 90MM DPC MICELLES; D2O	Resolution not provided
1D9L SOLUTION STRUCTURE OF CECROPIN A(1-8)-MAGAININ 2 HYBRID PEPTIDE ANALOGUE(P1) Deposited 1999-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 224–232（9 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.29；303 K；Pressure 1 NMR measurement conditions pH 4.29；298 K；Pressure 1 NMR sample composition 2MM PEPTIDE; 90MM DPC MICELLES; 90% H2O, 10% D2O NMR sample composition 2MM PEPTIDE; 90MM DPC MICELLES; D2O	Resolution not provided
1D9M SOLUTION STRUCTURE OF CECROPIN A(1-8)-MAGAININ 2 HYBRID PEPTIDE ANALOGUE(P2) Deposited 1999-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 223–232（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.78；303 K；Pressure 1 NMR measurement conditions pH 4.78；298 K；Pressure 1 NMR measurement conditions pH 4.78；318 K；Pressure 1 NMR sample composition 2MM PEPTIDE; 90MM DPC MICELLES; 90% H2O, 10% D2O NMR sample composition 2MM PEPTIDE; 90MM DPC MICELLES; D2O	Resolution not provided
1D9O SOLUTION STRUCTURE OF CECROPIN A(1-8)-MAGAININ 2(1-12) HYBRID PEPTIDE ANALOGUE(P3) Deposited 1999-10-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 129–140（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.05；303 K；Pressure 1 NMR measurement conditions pH 4.05；298 K；Pressure 1 NMR measurement conditions pH 4.05；318 K；Pressure 1 NMR sample composition 2MM PEPTIDE; 90MM DPC MICELLES; 90% H2O, 10% D2O NMR sample composition 2MM PEPTIDE; 90MM DPC MICELLES; D2O	Resolution not provided
1D9P SOLUTION STRUCTURE OF CECROPIN A(1-8)-MAGAININ 2(1-12) HYBRID PEPTIDE ANALOGUE(P4) Deposited 1999-10-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 129–140（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.64；298 K；Pressure 1 NMR measurement conditions pH 3.64；313 K；Pressure 1 NMR sample composition 2MM PEPTIDE; 90MM DPC MICELLES; 90% H2O, 10% D2O NMR sample composition 2MM PEPTIDE; 90MM DPC MICELLES; D2O	Resolution not provided
1DUM NMR STRUCTURE OF [F5Y, F16W] MAGAININ 2 BOUND TO PHOSPHOLIPID VESICLES Deposited 2000-01-18	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 129–151（23 aa） Chain B 129–151（23 aa）	Mutation：F5Y, F16W Mutation：F5Y, F16W	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；318 K；Ionic strength (raw mmCIF value) 50mM；Pressure ambient NMR sample composition 5mM [F5Y, F16W] magainin 2, 0.5mM DLPC-d64 \| 90% H2O/10% D2O	Resolution not provided
1F0D Cecropin A(1-8)-magainin 2(1-12) in dodecylphosphocholine micelles Deposited 2000-05-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 83–94（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.06；298 K NMR sample composition DODECYLPHOSPHOCHOLINE-d38 MICELLES \| 90% H2O/10% D2O	Resolution not provided
1F0E Cecropin A(1-8)-magainin 2(1-12) modified gig to P in dodecylphosphocholine micelles Deposited 2000-05-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 86–94（9 aa）	Mutation：GIG TO P IN MAGAININ SEGMENT Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.78；298 K NMR sample composition DODECYLPHOSPHOCHOLINE-d38 MICELLES \| 90% H2O/10% D2O	Resolution not provided
1F0F Cecropin A(1-8)-magainin 2(1-12) gig deletion modification in dodecylphosphocholine micelles Deposited 2000-05-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 86–94（9 aa）	Mutation：GIG DELETION IN MAGAININ SEGMENT Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.29；298 K NMR sample composition DODECYLPHOSPHOCHOLINE-d38 MICELLES \| 90% H2O/10% D2O	Resolution not provided
1F0G Cecropin A(1-8)-magainin 2(1-12) L2 in dodecylphosphocholine micelles Deposited 2000-05-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 83–94（12 aa）	Mutation：W28L Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.64；298 K NMR sample composition DODECYLPHOSPHOCHOLINE-d38 MICELLES \| 90% H2O/10% D2O	Resolution not provided
1F0H Cecropin A(1-8)-magainin 2(1-12) A2 in dodecylphosphocholine micelles Deposited 2000-05-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 83–94（12 aa）	Mutation：A28L Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.05；298 K NMR sample composition DODECYLPHOSPHOCHOLINE-d38 MICELLES \| 90% H2O/10% D2O	Resolution not provided
2LSA Magainin Deposited 2012-04-24	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 83–105（23 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 105；Pressure ambient NMR sample composition 1 mM magainin, 5 mM TRIS, 0.05 % TSP, 100 mM [U-2H] SDS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MAG NMR STRUCTURE OF MAGAININ 2 IN DPC MICELLES, 10 STRUCTURES Deposited 1997-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 267–289（23 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.1；303 K	Resolution not provided
4MGP Structure of racemic Ala-(8,13,18) Magainin 2 Deposited 2013-08-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 83–105（23 aa） Fragment：UNP residues 83-105	Mutation：S8A, G13A, G18A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Precipitant solution contained 0.1 M sodium citrate tribasic, pH 5.6, and 35% v/v tert-butanol. No additional cryoprotectant was necessary for vitrification of crystals in LN2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.233

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MAGA_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–23； UniProt 83–105

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9hvn
Deposition date deposition_date	2024-12-31
Structure title title	Atomic resolution crystal structure of the hexameric antimicrobial peptide Magainin-2
Keywords keywords	Antimicrobial peptide, peptide channel, atomic resolution, ANTIBIOTIC; ANTIBIOTIC
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	10.93 Å
Radius of gyration Rg (electron density) rg_electron	10.07 Å
Forward intensity I(0) i0	157220.00
Molecular weight molecular_weight	2381.0 kDa
Excluded volume excluded_volume	3074 Å³
Envelope volume envelope_volume	3588 Å³
Hydration-shell volume shell_volume	3797 Å³
Envelope diameter envelope_diameter	37.4 Å
Shell Rg shell_rg	13.36 Å
Envelope Rg envelope_rg	10.51 Å
Shape Rg shape_rg	9.98 Å
Total Rg total_rg	11.57 Å
Total atoms total_atoms	168
Residues n_residues	23
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	40.7 Å
Rg (real space) rg_real	11.14 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.5720e+05
I(0) uncertainty (real space) i0_real_error	1.7830e+03
Rg (reciprocal space) rg_reciprocal	11.13 Å
I(0) (reciprocal space) i0_reciprocal	157200.0000
Solution quality estimate total_estimate	0.7732
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	9.3 Å
Skewness Skewness skewness	0.538
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	7888.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.641; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.156; Smooth: 0.970

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

Unit-cell length a length_a	34.359 Å
Unit-cell length b length_b	34.359 Å
Unit-cell length c length_c	55.795 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	1.050 Å
Low-resolution limit resolution_low	29.756 Å
R factor r_factor	—
R_work r_work	0.1674
R_free r_free	0.1770

Description description	Magainins
Molecular weight formula_weight	2471.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	202

Atomic resolution crystal structure of the hexameric antimicrobial peptide Magainin-2

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

Magainins

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

fit	/app/data/saxs_computation/hv/9hvn/9hvn.fit
pddf	/app/data/pr_computation/hv/9hvn/9hvn.pr.out
profile	/app/data/saxs_computation/hv/9hvn/9hvn.dat