SAXSdb — 2l7l

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

Calmodulin

Homo sapiens

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–149	Not recorded	Calcium/calmodulin-dependent protein kinase type 1 × 1 （Q63450） CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions：pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR measurement conditions：pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient NMR sample composition：0.95 mM [U-13C; U-15N] protein, 1.05 mM peptide, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 20 mM Bis-Tris, 0.03 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.66 mM [U-2H; U-15N] protein, 0.40 mM peptide, 20 mM Bis-Tris, 100 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.64 mM 1H/13C-methyl Met; U-2H; U-15N protein, 0.83 mM peptide, 20 mM Bis-Tris, 100 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 100% D2O \| 100% D2O NMR sample composition：0.95 mM [U-13C; U-15N] protein, 1.05 mM peptide, 20 mM Bis-Tris, 300 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.95 mM [U-13C; U-15N] protein, 1.05 mM peptide, 20 mM Bis-Tris, 300 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 16 w/v Pf1 phage, 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.

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

View Construct and Data Evidence

UniProt name	B4DJ51_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–148； UniProt 2–149

Calcium/calmodulin-dependent protein kinase type 1

OrganismNot specified

UniProt Q63450

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 299–320	Fragment：Calmodulin-binding residues 299-320	Calmodulin × 1 （B4DJ51） CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions：pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR measurement conditions：pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient NMR sample composition：0.95 mM [U-13C; U-15N] protein, 1.05 mM peptide, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 20 mM Bis-Tris, 0.03 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.66 mM [U-2H; U-15N] protein, 0.40 mM peptide, 20 mM Bis-Tris, 100 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.64 mM 1H/13C-methyl Met; U-2H; U-15N protein, 0.83 mM peptide, 20 mM Bis-Tris, 100 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 100% D2O \| 100% D2O NMR sample composition：0.95 mM [U-13C; U-15N] protein, 1.05 mM peptide, 20 mM Bis-Tris, 300 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.95 mM [U-13C; U-15N] protein, 1.05 mM peptide, 20 mM Bis-Tris, 300 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 16 w/v Pf1 phage, 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 2L7L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A06 CALMODULIN-DEPENDENT PROTEIN KINASE FROM RAT Deposited 1997-12-09	Different construct 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 1–333（333 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.50 Å R-free 0.313
1MXE Structure of the Complex of Calmodulin with the Target Sequence of CaMKI Deposited 2002-10-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 294–318（25 aa） Fragment：Calmodulin Binding Domain	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；Cacodylate, Calcium chloride, MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.70 Å R-free 0.229
1MXE Structure of the Complex of Calmodulin with the Target Sequence of CaMKI Deposited 2002-10-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 294–318（25 aa） Fragment：Calmodulin Binding Domain	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；Cacodylate, Calcium chloride, MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.70 Å R-free 0.229

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KCC1A_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–22； UniProt 299–320

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	2l7l
Deposition date deposition_date	2010-12-13
Structure title title	Solution structure of Ca2+/calmodulin complexed with a peptide representing the calmodulin-binding domain of calmodulin kinase I
Keywords keywords	Calmodulin complex, calmodulin-peptide complex, CaMKI, Metal Binding Protein-Transferase complex; Metal Binding Protein/Transferase
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.92 Å
Radius of gyration Rg (electron density) rg_electron	15.57 Å
Forward intensity I(0) i0	7802060.00
Molecular weight molecular_weight	19448.0 kDa
Excluded volume excluded_volume	23877 Å³
Envelope volume envelope_volume	26883 Å³
Hydration-shell volume shell_volume	14616 Å³
Envelope diameter envelope_diameter	53.0 Å
Shell Rg shell_rg	21.38 Å
Envelope Rg envelope_rg	15.78 Å
Shape Rg shape_rg	15.58 Å
Total Rg total_rg	16.53 Å
Total atoms total_atoms	2647
Residues n_residues	170
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	52.7 Å
Rg (real space) rg_real	16.83 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	7.8020e+06
I(0) uncertainty (real space) i0_real_error	9.3810e+04
Rg (reciprocal space) rg_reciprocal	16.84 Å
I(0) (reciprocal space) i0_reciprocal	7802000.0000
Solution quality estimate total_estimate	0.8153
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.5 Å
Skewness Skewness skewness	0.195
Kurtosis Kurtosis kurtosis	-0.349
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1212000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Calmodulin
Molecular weight formula_weight	16721.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2647

ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Calcium/calmodulin-dependent protein kinase type 1
Molecular weight formula_weight	2606.1 kDa
EC 编号 ec_number	2.7.11.17
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AKSKWKQAFNATAVVRHMRKLQ

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	4

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8. Citations (1)

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fit	/app/data/saxs_computation/l7/2l7l/2l7l.fit
pddf	/app/data/pr_computation/l7/2l7l/2l7l.pr.out
profile	/app/data/saxs_computation/l7/2l7l/2l7l.dat

Solution structure of Ca2+/calmodulin complexed with a peptide representing the calmodulin-binding domain of calmodulin kinase I

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

Calcium/calmodulin-dependent protein kinase type 1

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)