SAXSdb — 1kxi

▼

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

CARDIOTOXIN V

Naja atra

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 22–83 Chain B； UniProt 22–83	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.19 Å R-free 0.305

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 1KXI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CVO THE SOLUTION STRUCTURE OF CARDIOTOXIN V FROM NAJA NAJA ATRA Deposited 1993-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–83（62 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CXH_NAJAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–62； UniProt 22–83 Author chain B； PDBConstruct 1–62； UniProt 22–83

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1kxi
Deposition date deposition_date	1996-08-29
Structure title title	STRUCTURE OF CYTOTOXIN HOMOLOG PRECURSOR
Keywords keywords	VENOM, CYTOTOXIN, CARDIOTOXIN, MULTIGENE FAMILY; CYTOTOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	14.87 Å
Radius of gyration Rg (electron density) rg_electron	14.61 Å
Forward intensity I(0) i0	3800500.00
Molecular weight molecular_weight	14047.0 kDa
Excluded volume excluded_volume	17769 Å³
Envelope volume envelope_volume	20718 Å³
Hydration-shell volume shell_volume	12166 Å³
Envelope diameter envelope_diameter	46.6 Å
Shell Rg shell_rg	20.10 Å
Envelope Rg envelope_rg	14.83 Å
Shape Rg shape_rg	14.67 Å
Total Rg total_rg	15.60 Å
Total atoms total_atoms	974
Residues n_residues	124
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	48.7 Å
Rg (real space) rg_real	14.79 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	3.8010e+06
I(0) uncertainty (real space) i0_real_error	4.6220e+04
Rg (reciprocal space) rg_reciprocal	14.80 Å
I(0) (reciprocal space) i0_reciprocal	3801000.0000
Solution quality estimate total_estimate	0.8898
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.3 Å
Skewness Skewness skewness	0.161
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1011000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.966

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1kxia_
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.1 — Snake venom toxins

Domain ID domain_id	d1kxib_
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.1 — Snake venom toxins

CATH v4.4 (2 domains)

Domain ID domain_id	1kxiA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	1kxiB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

▶

8. Citations (3)

▶

Unit-cell length a length_a	43.300 Å
Unit-cell length b length_b	43.300 Å
Unit-cell length c length_c	147.800 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.190 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.3050

Description description	CARDIOTOXIN V
Molecular weight formula_weight	7027.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1047

STRUCTURE OF CYTOTOXIN HOMOLOG PRECURSOR

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

CARDIOTOXIN V

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

Refinement Refinement

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Naja atra
通用名 common_name	Chinese cobra
NCBI Class编号 ncbi_taxonomy_id	8656
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

fit	/app/data/saxs_computation/kx/1kxi/1kxi.fit
pddf	/app/data/pr_computation/kx/1kxi/1kxi.pr.out
profile	/app/data/saxs_computation/kx/1kxi/1kxi.dat