1agg

THE SOLUTION STRUCTURE OF OMEGA-AGA-IVB, A P-TYPE CALCIUM CHANNEL ANTAGONIST FROM THE VENOM OF AGELENOPSIS APERTA

Method: SOLUTION NMR D_max: 29.5 Å Quality: REASONABLE

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

OMEGA-AGATOXIN-IVB

OrganismNot specified

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 36–83	Not recorded	No other associated polymer	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	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 1AGG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OMA SEQUENTIAL ASSIGNMENT AND STRUCTURE DETERMINATION OF SPIDER TOXIN OMEGA-AGA-IVB Deposited 1993-09-09	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–83（48 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1OMB SEQUENTIAL ASSIGNMENT AND STRUCTURE DETERMINATION OF SPIDER TOXIN OMEGA-AGA-IVB Deposited 1993-09-09	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–83（48 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	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	TOG4B_AGEAP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–48； UniProt 36–83

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1agg
Deposition date deposition_date	1995-11-03
Structure title title	THE SOLUTION STRUCTURE OF OMEGA-AGA-IVB, A P-TYPE CALCIUM CHANNEL ANTAGONIST FROM THE VENOM OF AGELENOPSIS APERTA
Keywords keywords	NEUROTOXIN, P-TYPE CALCIUM CHANNEL ANTAGONIST; NEUROTOXIN
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	11.15 Å
Radius of gyration Rg (electron density) rg_electron	11.60 Å
Forward intensity I(0) i0	297698000.00
Molecular weight molecular_weight	126750.0 kDa
Excluded volume excluded_volume	151450 Å³
Envelope volume envelope_volume	29611 Å³
Hydration-shell volume shell_volume	15087 Å³
Envelope diameter envelope_diameter	53.3 Å
Shell Rg shell_rg	22.75 Å
Envelope Rg envelope_rg	17.56 Å
Shape Rg shape_rg	11.63 Å
Total Rg total_rg	11.91 Å
Total atoms total_atoms	16752
Residues n_residues	1152
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	29.5 Å
Rg (real space) rg_real	10.49 Å
Rg uncertainty (real space) rg_real_error	0.04 Å
I(0) (real space) i0_real	2.8440e+08
I(0) uncertainty (real space) i0_real_error	2.1560e+06
Rg (reciprocal space) rg_reciprocal	11.27 Å
I(0) (reciprocal space) i0_reciprocal	297700000.0000
Solution quality estimate total_estimate	0.6858
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.303
Kurtosis Kurtosis kurtosis	-0.511
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	4.9820
Highest regularization parameter α highest_alpha	67490.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.999; Stabil: 0.976; Sysdev: 0.000; Positv: 1.000; Valcen: 0.991; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1agga_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.6 — omega toxin-like
Family Family family	g.3.6.2 — Spider toxins

CATH v4.4 (1 domains)

Domain ID domain_id	1aggA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	40 — Omega-AgatoxinV
Homologous superfamily homologous superfamily	10 —

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8. Citations (3)

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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	OMEGA-AGATOXIN-IVB
Molecular weight formula_weight	5287.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	16752

fit	/app/data/saxs_computation/ag/1agg/1agg.fit
pddf	/app/data/pr_computation/ag/1agg/1agg.pr.out
profile	/app/data/saxs_computation/ag/1agg/1agg.dat

THE SOLUTION STRUCTURE OF OMEGA-AGA-IVB, A P-TYPE CALCIUM CHANNEL ANTAGONIST FROM THE VENOM OF AGELENOPSIS APERTA

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

OMEGA-AGATOXIN-IVB

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

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)