SAXSdb — 1byy

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

PROTEIN (SODIUM CHANNEL ALPHA-SUBUNIT)

Rattus norvegicus

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 1474–1526	Fragment：INACTIVATION DOMAIN FRAGMENT	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；299 K NMR sample composition：H2O/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 1BYY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KXW Structure of the C-domain Fragment of apo Calmodulin Bound to the IQ motif of Nav1.2 Deposited 2010-05-13	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1901–1927（27 aa） Fragment：IQ-motif of the Voltage-dependent Sodium Channel (UNP Residues 1901-1927)	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 ambient NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] C-domain of apo Calmodulin, 1.5 mM Voltage-dependent Sodium Channel v 1.2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM Voltage-dependent Sodium Channel v 1.2, 1.5 mM [U-100% 13C; U-100% 15N] C-domain of apo Calmodulin, 100% D2O \| 100% D2O	Resolution not provided
2M5E Structure of the C-domain of Calcium-saturated Calmodulin bound to the IQ motif of NaV1.2 Deposited 2013-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1901–1927（27 aa） Fragment：UNP residues 1901-1927	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] C-domain of Calmodulin, 1.5 mM IQ motif peptide of NaV1.2, 3.3 mM CALCIUM ION, 10 mM [U-2H] imidazole, 100 mM potassium chloride, 0.01 % sodium azide, 50 uM [U-2H] EDTA, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] C-domain of Calmodulin, 1.5 mM IQ motif peptide of NaV1.2, 3.3 mM CALCIUM ION, 10 mM [U-2H] imidazole, 100 mM potassium chloride, 0.01 % sodium azide, 50 uM [U-2H] EDTA, 100% D2O \| 100% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	SCN2A_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–53； UniProt 1474–1526

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	1byy
Deposition date deposition_date	1998-10-21
Structure title title	SODIUM CHANNEL IIA INACTIVATION GATE
Keywords keywords	SODIUM CHANNEL, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	9.50 Å
Radius of gyration Rg (electron density) rg_electron	9.56 Å
Forward intensity I(0) i0	9690770.00
Molecular weight molecular_weight	25369.0 kDa
Excluded volume excluded_volume	31938 Å³
Envelope volume envelope_volume	8275 Å³
Hydration-shell volume shell_volume	6747 Å³
Envelope diameter envelope_diameter	40.7 Å
Shell Rg shell_rg	15.96 Å
Envelope Rg envelope_rg	11.93 Å
Shape Rg shape_rg	9.56 Å
Total Rg total_rg	10.17 Å
Total atoms total_atoms	3420
Residues n_residues	210
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	41.6 Å
Rg (real space) rg_real	9.65 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	9.6910e+06
I(0) uncertainty (real space) i0_real_error	1.2280e+05
Rg (reciprocal space) rg_reciprocal	9.64 Å
I(0) (reciprocal space) i0_reciprocal	9691000.0000
Solution quality estimate total_estimate	0.7043
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	8.4 Å
Skewness Skewness skewness	0.498
Kurtosis Kurtosis kurtosis	-0.244
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4739.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.372; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.041; Smooth: 0.997

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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

SCOP 2.08 (1 domains)

Domain ID domain_id	d1byya_
Class class	j — Peptides
Fold Fold fold	j.12 — Inactivation gate of potassium and sodium channels
Superfamily Superfamily superfamily	j.12.1 — Inactivation gate of potassium and sodium channels
Family Family family	j.12.1.1 — Inactivation gate of potassium and sodium channels

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

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

Description description	PROTEIN (SODIUM CHANNEL ALPHA-SUBUNIT)
Molecular weight formula_weight	6266.3 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	3420

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

SODIUM CHANNEL IIA INACTIVATION GATE

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

PROTEIN (SODIUM CHANNEL ALPHA-SUBUNIT)

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/by/1byy/1byy.fit
pddf	/app/data/pr_computation/by/1byy/1byy.pr.out
profile	/app/data/saxs_computation/by/1byy/1byy.dat