SAXSdb — 8aht

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

Calmodulin

Plasmodium falciparum

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 × 3 PDB declaration: dimeric（2） Count mismatch; review required	Chain A； UniProt 1–149 Chain B； UniProt 1–149 Chain C； UniProt 1–149	Not recorded	CA CALCIUM ION × 12	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
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: dimeric（2） Count mismatch; review required	Chain A； UniProt 1–149 Chain B； UniProt 1–149 Chain C； UniProt 1–149 Chain D； UniProt 1–149	Not recorded	CA CALCIUM ION × 16	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
3	Protein homooligomer Homooligomer Protein × 3 PDB declaration: dimeric（2） Count mismatch; review required	Chain A； UniProt 1–149 Chain B； UniProt 1–149 Chain D； UniProt 1–149	Not recorded	CA CALCIUM ION × 12	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
4	Protein heterocomplex Heteromer Protein × 6 PDB declaration: dimeric（2） Count mismatch; review required	Chain A； UniProt 1–149 Chain B； UniProt 1–149	Not recorded	Melittin × 4 （P01501） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CALM_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 1–149 Author chain B； PDBConstruct 1–149； UniProt 1–149 Author chain C； PDBConstruct 1–149； UniProt 1–149 Author chain D； PDBConstruct 1–149； UniProt 1–149

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
4	Protein heterocomplex Heteromer Protein × 6 PDB declaration: dimeric（2） Count mismatch; review required	Chain F； UniProt 44–69 Chain G； UniProt 44–69 Chain H； UniProt 44–69 Chain I； UniProt 44–69	Not recorded	Calmodulin × 2 （P62203） 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

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 8AHT	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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 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 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 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

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	2
Chains and sequence ranges	Author chain F； PDBConstruct 1–26； UniProt 44–69 Author chain G； PDBConstruct 1–26； UniProt 44–69 Author chain H； PDBConstruct 1–26； UniProt 44–69 Author chain I； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8aht
Deposition date deposition_date	2022-07-22
Structure title title	Crystal structure of Plasmodium falciparum Ca2+/Calmodulin in complex with melittin
Keywords keywords	hub protein, linear recognition motif, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	29.63 Å
Radius of gyration Rg (electron density) rg_electron	28.64 Å
Forward intensity I(0) i0	81980800.00
Molecular weight molecular_weight	68836.0 kDa
Excluded volume excluded_volume	85068 Å³
Envelope volume envelope_volume	111850 Å³
Hydration-shell volume shell_volume	32941 Å³
Envelope diameter envelope_diameter	102.9 Å
Shell Rg shell_rg	35.46 Å
Envelope Rg envelope_rg	28.43 Å
Shape Rg shape_rg	28.66 Å
Total Rg total_rg	29.24 Å
Total atoms total_atoms	9208
Residues n_residues	644
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	95.6 Å
Rg (real space) rg_real	29.53 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	8.1980e+07
I(0) uncertainty (real space) i0_real_error	1.2870e+06
Rg (reciprocal space) rg_reciprocal	29.58 Å
I(0) (reciprocal space) i0_reciprocal	81980000.0000
Solution quality estimate total_estimate	0.9052
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.9 Å
Skewness Skewness skewness	0.175
Kurtosis Kurtosis kurtosis	-0.513
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11550000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Calmodulin
Molecular weight formula_weight	16946.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9492

MADKLTEEQISEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEIDTDGNGTIDFPEFLTLMARKLKDTDTEEELIEAFRVFDRDGDGYISADELRHVMTNLGEKLTNEEVDEMIREADIDGDGQINYEEFVKMMIAK

来源 Source

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI Class编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Melittin
Molecular weight formula_weight	2852.5 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G,H,I

GIGAVLKVLTTGLPALISWIKRKRQQ

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8ahtA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	8ahtB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Unit-cell length a length_a	37.900 Å
Unit-cell length b length_b	60.680 Å
Unit-cell length c length_c	68.450 Å
Unit-cell angle α angle_alpha	95.77 °
Unit-cell angle β angle_beta	89.99 °
Unit-cell angle γ angle_gamma	97.05 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	47.430 Å
R factor r_factor	0.2356
R_work r_work	0.2341
R_free r_free	0.2661

fit	/app/data/saxs_computation/ah/8aht/8aht.fit
pddf	/app/data/pr_computation/ah/8aht/8aht.pr.out
profile	/app/data/saxs_computation/ah/8aht/8aht.dat

Crystal structure of Plasmodium falciparum Ca2+/Calmodulin in complex with melittin

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

Calmodulin

State in the Current Structure

Other States of the Same Protein in the Database

Melittin

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)