SAXSdb — 2p4l

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

I-superfamily conotoxin r11a

Conus radiatus

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 1–46	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.9；298 K；Pressure AMBIENT NMR sample composition：1.1mM [L-Phe44] iota-RXIA-, 95% H2O, 5% D2O \| 95% H2O/5% 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 2P4L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
25II Cryo-EM structure of human Nav1.6 in complex with Iota-Conotoxin RXIA Deposited 2026-04-06	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 D 1–46（46 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Y01 CHOLESTEROL HEMISUCCINATE × 3 CLR CHOLESTEROL × 1 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 P3X (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate × 1 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
2JRY Structure and Sodium Channel Activity of an Excitatory I1-Superfamily Conotoxin Deposited 2007-06-29	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–46（46 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.9；298 K；Pressure ambient NMR sample composition 0.8 mM conotoxin Iota-RXIA, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2JTU NMR structure of iota-RXIA(38) Deposited 2007-08-06	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–38（38 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.9；298 K；Pressure ambient NMR sample composition 0.6 mM iota-RXIA, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	CXI6_CONRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–46； UniProt 1–46

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	2p4l
Deposition date deposition_date	2007-03-12
Structure title title	Structure and sodium channel activity of an excitatory I1-superfamily conotoxin
Keywords keywords	;IAA, iodoacetic acid; INa, sodium current; NEM, N-ethylmaleimide; NMR, nuclear magnetic resonance; NOE, nuclear Overhauser effect; TFA, trifluoroacetic acid; VGSC, voltage-gated sodium channel., TOXIN ;; TOXIN
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	10.58 Å
Radius of gyration Rg (electron density) rg_electron	11.83 Å
Forward intensity I(0) i0	167305000.00
Molecular weight molecular_weight	99714.0 kDa
Excluded volume excluded_volume	121160 Å³
Envelope volume envelope_volume	29141 Å³
Hydration-shell volume shell_volume	14975 Å³
Envelope diameter envelope_diameter	54.9 Å
Shell Rg shell_rg	22.44 Å
Envelope Rg envelope_rg	17.13 Å
Shape Rg shape_rg	11.93 Å
Total Rg total_rg	12.02 Å
Total atoms total_atoms	13040
Residues n_residues	860
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	27.8 Å
Rg (real space) rg_real	9.94 Å
Rg uncertainty (real space) rg_real_error	0.04 Å
I(0) (real space) i0_real	1.6030e+08
I(0) uncertainty (real space) i0_real_error	1.0890e+06
Rg (reciprocal space) rg_reciprocal	10.72 Å
I(0) (reciprocal space) i0_reciprocal	167300000.0000
Solution quality estimate total_estimate	0.6872
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	11.2 Å
Skewness Skewness skewness	0.287
Kurtosis Kurtosis kurtosis	-0.561
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	4.0550
Highest regularization parameter α highest_alpha	23000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 1.000; Stabil: 0.987; Sysdev: 0.000; Positv: 1.000; Valcen: 0.974; 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	2p4lA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	40 — Omega-AgatoxinV
Homologous superfamily homologous superfamily	80 —

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8. Citations (1)

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Description description	I-superfamily conotoxin r11a
Molecular weight formula_weight	4987.7 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	13040

来源生物 organism	Conus radiatus
NCBI Class编号 ncbi_taxonomy_id	61198
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/p4/2p4l/2p4l.fit
pddf	/app/data/pr_computation/p4/2p4l/2p4l.pr.out
profile	/app/data/saxs_computation/p4/2p4l/2p4l.dat

Structure and sodium channel activity of an excitatory I1-superfamily conotoxin

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

I-superfamily conotoxin r11a

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)