SAXSdb — 1cdt

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

CARDIOTOXIN VII4

Naja mossambica

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 1–60 Chain B； UniProt 1–60	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CX4_NAJMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–60； UniProt 1–60 Author chain B； PDBConstruct 1–60； UniProt 1–60

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	1cdt
Deposition date deposition_date	1990-05-17
Structure title title	CARDIOTOXIN V4/II FROM NAJA MOSSAMBICA MOSSAMBICA: THE REFINED CRYSTAL STRUCTURE
Keywords keywords	CYTOTOXIN; CYTOTOXIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	14.78 Å
Radius of gyration Rg (electron density) rg_electron	14.36 Å
Forward intensity I(0) i0	3819610.00
Molecular weight molecular_weight	13641.0 kDa
Excluded volume excluded_volume	17060 Å³
Envelope volume envelope_volume	19339 Å³
Hydration-shell volume shell_volume	11496 Å³
Envelope diameter envelope_diameter	46.8 Å
Shell Rg shell_rg	19.93 Å
Envelope Rg envelope_rg	14.78 Å
Shape Rg shape_rg	14.39 Å
Total Rg total_rg	15.39 Å
Total atoms total_atoms	930
Residues n_residues	120
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	48.6 Å
Rg (real space) rg_real	14.72 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	3.8200e+06
I(0) uncertainty (real space) i0_real_error	3.7850e+04
Rg (reciprocal space) rg_reciprocal	14.72 Å
I(0) (reciprocal space) i0_reciprocal	3820000.0000
Solution quality estimate total_estimate	0.8923
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.3 Å
Skewness Skewness skewness	0.174
Kurtosis Kurtosis kurtosis	-0.472
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1152000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.969

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CARDIOTOXIN VII4
Molecular weight formula_weight	6727.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	978

LKCNKLIPIAYKTCPEGKNLCYKMMLASKKMVPVKRGCINVCPKNSALVKYVCCSTDRCN

来源 Source

来源生物 organism	Naja mossambica
通用名 common_name	Mozambique cobra
NCBI Class编号 ncbi_taxonomy_id	8644

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	48

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cdta_
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	d1cdtb_
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	1cdtA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	1cdtB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

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8. Citations (2)

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Unit-cell length a length_a	73.900 Å
Unit-cell length b length_b	73.900 Å
Unit-cell length c length_c	59.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	5.000 Å
R factor r_factor	0.1970
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/cd/1cdt/1cdt.fit
pddf	/app/data/pr_computation/cd/1cdt/1cdt.pr.out
profile	/app/data/saxs_computation/cd/1cdt/1cdt.dat

CARDIOTOXIN V4/II FROM NAJA MOSSAMBICA MOSSAMBICA: THE REFINED CRYSTAL STRUCTURE

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

CARDIOTOXIN VII4

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