SAXSdb — 1v6p

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

Cobrotoxin

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 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	CU COPPER (II) ION × 12 CL CHLORIDE ION × 1 NA SODIUM ION × 2 EOH ETHANOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；HAc-NaAc, Ethanol, NaCl, CuCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 0.87 Å R-free 0.153

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 1V6P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1COE SOLUTION CONFORMATION OF COBROTOXIN: A NUCLEAR MAGNETIC RESONANCE AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING STUDY Deposited 1994-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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	NXS1_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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1v6p
Deposition date deposition_date	2003-12-03
Structure title title	Crystal structure of Cobrotoxin
Keywords keywords	atomic resolution, short-chain neurotoxin, Naja atra, Copper ion, TOXIN; TOXIN
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	16.12 Å
Radius of gyration Rg (electron density) rg_electron	15.25 Å
Forward intensity I(0) i0	6482640.00
Molecular weight molecular_weight	14855.0 kDa
Excluded volume excluded_volume	16934 Å³
Envelope volume envelope_volume	21020 Å³
Hydration-shell volume shell_volume	12007 Å³
Envelope diameter envelope_diameter	57.6 Å
Shell Rg shell_rg	20.62 Å
Envelope Rg envelope_rg	15.63 Å
Shape Rg shape_rg	15.18 Å
Total Rg total_rg	16.29 Å
Total atoms total_atoms	981
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

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

Maximum dimension Dmax dmax	56.0 Å
Rg (real space) rg_real	16.08 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	6.4830e+06
I(0) uncertainty (real space) i0_real_error	7.9610e+04
Rg (reciprocal space) rg_reciprocal	16.08 Å
I(0) (reciprocal space) i0_reciprocal	6483000.0000
Solution quality estimate total_estimate	0.7943
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.6 Å
Skewness Skewness skewness	0.253
Kurtosis Kurtosis kurtosis	-0.341
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1426000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Cobrotoxin
Molecular weight formula_weight	6967.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1476

LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ETHANOL
Molecular weight formula_weight	46.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	248

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1v6pa_
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	d1v6pb_
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	1v6pA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	1v6pB00
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 (1)

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Unit-cell length a length_a	46.808 Å
Unit-cell length b length_b	47.287 Å
Unit-cell length c length_c	90.018 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	0.870 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1195
R_free r_free	0.1533

fit	/app/data/saxs_computation/v6/1v6p/1v6p.fit
pddf	/app/data/pr_computation/v6/1v6p/1v6p.pr.out
profile	/app/data/saxs_computation/v6/1v6p/1v6p.dat

Crystal structure of Cobrotoxin

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

Cobrotoxin

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

Diffraction experiment Diffraction