SAXSdb — 4om4

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

Cytotoxin 2

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 22–81 Chain B； UniProt 22–81 Chain C； UniProt 22–81 Chain D； UniProt 22–81 Chain E； UniProt 22–81	Fragment：UNP residues 22-81	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；5.5 M ammonium nitrate, 0.1 M Bis-Tris, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.74 Å R-free 0.260

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 4OM4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CRE CARDIOTOXIN II FROM TAIWAN COBRA VENOM, NAJA NAJA ATRA: STRUCTURE IN SOLUTION AND COMPARISION AMONG HOMOLOGOUS CARDIOTOXINS Deposited 1994-03-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–81（60 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CRF CARDIOTOXIN II FROM TAIWAN COBRA VENOM, NAJA NAJA ATRA: STRUCTURE IN SOLUTION AND COMPARISION AMONG HOMOLOGOUS CARDIOTOXINS Deposited 1994-03-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–81（60 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	CTXA2_NAJAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–60； UniProt 22–81 Author chain B； PDBConstruct 1–60； UniProt 22–81 Author chain C； PDBConstruct 1–60； UniProt 22–81 Author chain D； PDBConstruct 1–60； UniProt 22–81 Author chain E； PDBConstruct 1–60； UniProt 22–81

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	4om4
Deposition date deposition_date	2014-01-26
Structure title title	Crystal structure of CTX A2 from Taiwan Cobra (Naja naja atra)
Keywords keywords	Five beta sheets, three functional loops, endocytosis, heparin, heparan sulfate, 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	23.19 Å
Radius of gyration Rg (electron density) rg_electron	22.50 Å
Forward intensity I(0) i0	19452800.00
Molecular weight molecular_weight	33791.0 kDa
Excluded volume excluded_volume	42653 Å³
Envelope volume envelope_volume	53646 Å³
Hydration-shell volume shell_volume	20753 Å³
Envelope diameter envelope_diameter	81.8 Å
Shell Rg shell_rg	28.32 Å
Envelope Rg envelope_rg	22.29 Å
Shape Rg shape_rg	22.48 Å
Total Rg total_rg	23.37 Å
Total atoms total_atoms	2325
Residues n_residues	300
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	79.5 Å
Rg (real space) rg_real	23.13 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	1.9450e+07
I(0) uncertainty (real space) i0_real_error	3.0250e+05
Rg (reciprocal space) rg_reciprocal	23.14 Å
I(0) (reciprocal space) i0_reciprocal	19450000.0000
Solution quality estimate total_estimate	0.8762
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.217
Kurtosis Kurtosis kurtosis	-0.263
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	780800.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d4om4a_
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	d4om4b_
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	d4om4c_
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	d4om4d_
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	d4om4e_
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 (5 domains)

Domain ID domain_id	4om4A00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	4om4B00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	4om4C00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	4om4D00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	4om4E00
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	107.412 Å
Unit-cell length b length_b	107.412 Å
Unit-cell length c length_c	100.256 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	40

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.740 Å
Low-resolution limit resolution_low	25.620 Å
R factor r_factor	0.1998
R_work r_work	0.1966
R_free r_free	0.2596

Description description	Cytotoxin 2
Molecular weight formula_weight	6760.2 kDa
Source method src_method	nat
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	2417

Crystal structure of CTX A2 from Taiwan Cobra (Naja naja atra)

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

Cytotoxin 2

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	92

fit	/app/data/saxs_computation/om/4om4/4om4.fit
pddf	/app/data/pr_computation/om/4om4/4om4.pr.out
profile	/app/data/saxs_computation/om/4om4/4om4.dat