SAXSdb — 2kav

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

Sodium channel protein type 2 subunit alpha

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1777–1882	Fragment：C-terminal EF-Hand Domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.4；290.5 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：0.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM [D5-98%] glycine, 20 mM [D11-98 %] TRIS, 0.1 mM [D16-98%] EDTA, 10 % [U-99% 2H] D2O, 1 mM [D10-98%] DTT, 0.02 % NaN3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.5 mM [U-10% 13C; U-99% 15N] protein, 100 mM [D5-98%] glycine, 20 mM [D11-98 %] TRIS, 0.1 mM [D16-98%] EDTA, 10 % [U-99% 2H] D2O, 1 mM [D10-98%] DTT, 0.02 % NaN3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM [D5-98%] glycine, 20 mM [D11-98 %] TRIS, 0.1 mM [D16-98%] EDTA, 10 % [U-99% 2H] D2O, 1 mM [D10-98%] DTT, 0.02 % NaN3, 15 mg 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 2KAV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4JPZ Voltage-gated sodium channel 1.2 C-terminal domain in complex with FGF13U and Ca2+/calmodulin Deposited 2013-03-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1777–1937（161 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；290 K；14% pEG3350, 300 mM sodium acetate,50 mM Tris pH 7.5, and 2 mM CaCl2, EVAPORATION, temperature 290K	Resolution 3.02 Å R-free 0.246
4JPZ Voltage-gated sodium channel 1.2 C-terminal domain in complex with FGF13U and Ca2+/calmodulin Deposited 2013-03-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1777–1937（161 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；290 K；14% pEG3350, 300 mM sodium acetate,50 mM Tris pH 7.5, and 2 mM CaCl2, EVAPORATION, temperature 290K	Resolution 3.02 Å R-free 0.246
6BUT Solution structure of full-length apo mammalian calmodulin bound to the IQ motif of the human voltage-gated sodium channel NaV1.2 Deposited 2017-12-11	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1901–1927（27 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 0.950 mM U-99% C13, U-99% N15 Calmodulin, 0.950 mM U-99% C13, U-99% N15 voltage-gated sodium channel NaV1.2 IQ motif, 0.1 mM U-98% 2H EDTA, 100 mM KCl, 10 mM [U-99% 2H] imidazole, 0.01 % w/v sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.95 mM U-99% C13, U-99% N15 Calmodulin, 0.95 mM U-99% C13, U-99% N15 voltage-gated sodium channel NaV1.2 IQ motif, 0.1 mM U-98% 2H EDTA, 100 mM potassium chloride, 10 mM [U-99% 2H] imidazole, 0.01 % w/v sodium azide, 100% D2O \| 100% D2O	Resolution not provided
6J8E Human Nav1.2-beta2-KIIIA ternary complex Deposited 2019-01-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–2005（2005 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 5.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SCN2A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–129； UniProt 1777–1882

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	2kav
Deposition date deposition_date	2008-11-15
Structure title title	Solution structure of the human Voltage-gated Sodium Channel, brain isoform (Nav1.2)
Keywords keywords	;Voltage-gated Sodium Channel, Alternative splicing, Disease mutation, Epilepsy, Glycoprotein, Ion transport, Ionic channel, Membrane, Polymorphism, Sodium, Sodium channel, Sodium transport, Transmembrane, Transport, Ubl conjugation, Voltage-gated channel, TRANSPORT PROTEIN, TRANSPORT PROTEIN REGULATOR ;; TRANSPORT PROTEIN REGULATOR
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	17.23 Å
Radius of gyration Rg (electron density) rg_electron	16.44 Å
Forward intensity I(0) i0	456636000.00
Molecular weight molecular_weight	181580.0 kDa
Excluded volume excluded_volume	227500 Å³
Envelope volume envelope_volume	52353 Å³
Hydration-shell volume shell_volume	20598 Å³
Envelope diameter envelope_diameter	65.7 Å
Shell Rg shell_rg	28.49 Å
Envelope Rg envelope_rg	22.66 Å
Shape Rg shape_rg	16.42 Å
Total Rg total_rg	16.94 Å
Total atoms total_atoms	25005
Residues n_residues	1590
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	59.4 Å
Rg (real space) rg_real	17.31 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	4.5660e+08
I(0) uncertainty (real space) i0_real_error	5.7930e+06
Rg (reciprocal space) rg_reciprocal	17.30 Å
I(0) (reciprocal space) i0_reciprocal	456600000.0000
Solution quality estimate total_estimate	0.7530
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	52.4 Å
Skewness Skewness skewness	0.445
Kurtosis Kurtosis kurtosis	-0.235
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	397100.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.630; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.896; 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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2kavA01
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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Description description	Sodium channel protein type 2 subunit alpha
Molecular weight formula_weight	14591.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	25005

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

fit	/app/data/saxs_computation/ka/2kav/2kav.fit
pddf	/app/data/pr_computation/ka/2kav/2kav.pr.out
profile	/app/data/saxs_computation/ka/2kav/2kav.dat

Solution structure of the human Voltage-gated Sodium Channel, brain isoform (Nav1.2)

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

Sodium channel protein type 2 subunit alpha

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)