SAXSdb — 9gcn

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

Alpha-cobratoxin

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain Z； UniProt 1–71	Not recorded	Protein. Variable Domain of Heavy-Chain only Antibodies (VHH) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298.15 K；1.5 mM Tris and 6.5 mM NaCl, 17% (w/v) PEG1500. 20% (v/v) glycerol as cryopreservative.	Resolution 3.00 Å R-free 0.292
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain Y； UniProt 1–71	Not recorded	Protein. Variable Domain of Heavy-Chain only Antibodies (VHH) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298.15 K；1.5 mM Tris and 6.5 mM NaCl, 17% (w/v) PEG1500. 20% (v/v) glycerol as cryopreservative.	Resolution 3.00 Å R-free 0.292
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain V； UniProt 1–71	Not recorded	Protein. Variable Domain of Heavy-Chain only Antibodies (VHH) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298.15 K；1.5 mM Tris and 6.5 mM NaCl, 17% (w/v) PEG1500. 20% (v/v) glycerol as cryopreservative.	Resolution 3.00 Å R-free 0.292
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain X； UniProt 1–71	Not recorded	Protein. Variable Domain of Heavy-Chain only Antibodies (VHH) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298.15 K；1.5 mM Tris and 6.5 mM NaCl, 17% (w/v) PEG1500. 20% (v/v) glycerol as cryopreservative.	Resolution 3.00 Å R-free 0.292

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 9GCN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CTX THREE-DIMENSIONAL STRUCTURE OF THE-LONG-NEUROTOXIN FROM COBRA VENOM Deposited 1982-04-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–71（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1LXG Solution structure of alpha-cobratoxin complexed with a cognate peptide (structure ensemble) Deposited 2002-06-05	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–71（71 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；308 K；Pressure AMBIENT NMR sample composition 1.6 mM alpha-cobratoxin/alpha18-mer complex, alpha18-mer is U-15N, 50 mM perdeuterated potassium acetate buffer (pH 4.0) with 5% D2O and 0.05% sodium azide \| 95% H2O/5% D2O	Resolution not provided
1LXH Solution structure of alpha-cobratoxin complexed with a cognate peptide (minimized average structure) Deposited 2002-06-05	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–71（71 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；308 K；Ionic strength (raw mmCIF value) NULL；Pressure AMBIENT NMR sample composition 1.6 mM alpha-cobratoxin/alpha18-mer complex, alpha18-mer is U-15N, 50 mM perdeuterated potassium acetate buffer (pH 4.0) with 5% D2O and 0.05% sodium azide \| 95% H2O/5% D2O	Resolution not provided
1YI5 Crystal structure of the a-cobratoxin-AChBP complex Deposited 2005-01-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain F 1–71（71 aa） Chain G 1–71（71 aa） Chain H 1–71（71 aa） Chain I 1–71（71 aa） Chain J 1–71（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.9M NA-CITRATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 4.20 Å R-free 0.378
4AEA Dimeric alpha-cobratoxin X-ray structure: Localization of intermolecular disulfides and possible mode of binding to nicotinic acetylcholine receptors Deposited 2012-01-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–71（71 aa）	Not recorded	GLY GLYCINE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 2；60% (V/V) 2-METHYL-2,4- PENTANEDIOL, 0.1 M GLYCINE-HCL PH 2	Resolution 1.94 Å R-free 0.251
4AEA Dimeric alpha-cobratoxin X-ray structure: Localization of intermolecular disulfides and possible mode of binding to nicotinic acetylcholine receptors Deposited 2012-01-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–71（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 2；60% (V/V) 2-METHYL-2,4- PENTANEDIOL, 0.1 M GLYCINE-HCL PH 2	Resolution 1.94 Å R-free 0.251
6ZFM Structure of alpha-Cobratoxin with a peptide inhibitor Deposited 2020-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–71（71 aa） Chain B 1–71（71 aa） Chain D 1–71（71 aa） Chain E 1–71（71 aa）	Not recorded	QJE 3-[2-[2-[2-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]propan-1-ol × 2 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M Carboxylic acids (sodium formate / ammonium acetate / sodium citrate / sodium potassium tartrate / sodium oxamate), 0.1 M HEPES / MOPS pH7.5, 30.0 % v/v PEG 500 MME / PEG 20000	Resolution 1.90 Å R-free 0.230
7PC0 GABA-A receptor bound by a-Cobratoxin Deposited 2021-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain K 1–71（71 aa） Chain L 1–71（71 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 HSM HISTAMINE × 1 ZN ZINC ION × 1 HEX HEXANE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7ULG recombinant alpha cobra toxin Deposited 2022-04-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–71（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；291.15 K；110 mg/ml in 200 mM NH4Ac (pH 7.0/25 DC), 1:1 with 0.1 M HEPES (pH 7.9), 30% Jeffamine M-600 (pH 7.0), 18 DC	Resolution 1.57 Å R-free 0.181
7ULG recombinant alpha cobra toxin Deposited 2022-04-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–71（71 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；291.15 K；110 mg/ml in 200 mM NH4Ac (pH 7.0/25 DC), 1:1 with 0.1 M HEPES (pH 7.9), 30% Jeffamine M-600 (pH 7.0), 18 DC	Resolution 1.57 Å R-free 0.181
7ULG recombinant alpha cobra toxin Deposited 2022-04-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–71（71 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；291.15 K；110 mg/ml in 200 mM NH4Ac (pH 7.0/25 DC), 1:1 with 0.1 M HEPES (pH 7.9), 30% Jeffamine M-600 (pH 7.0), 18 DC	Resolution 1.57 Å R-free 0.181
7ULG recombinant alpha cobra toxin Deposited 2022-04-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–71（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；291.15 K；110 mg/ml in 200 mM NH4Ac (pH 7.0/25 DC), 1:1 with 0.1 M HEPES (pH 7.9), 30% Jeffamine M-600 (pH 7.0), 18 DC	Resolution 1.57 Å R-free 0.181
9BK5 Structure of LNG binder complex Deposited 2024-04-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–71（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.5 M Ammonium Sulfate and 25% (v/v) glycerol	Resolution 2.68 Å R-free 0.268
9FYT mAbs in complex with cobratoxin at pH 4.5 Deposited 2024-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–71（71 aa） Chain B 1–71（71 aa）	Not recorded	CL CHLORIDE ION × 3 GOL GLYCEROL × 5 SO4 SULFATE ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M Bis-Tris pH 6.5, 0.2 M Ammonium Sulfate, 25% PEG 3350	Resolution 1.55 Å R-free 0.237
9HUO A01 mAbs bound to cobratoxin at pH 5.5 Deposited 2024-12-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–71（71 aa）	Not recorded	GOL GLYCEROL × 2 CL CHLORIDE ION × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；25% PEG3350, 0.1M Bis-Tris pH5.5, 0.25 M AmS	Resolution 1.60 Å R-free 0.225
9HUO A01 mAbs bound to cobratoxin at pH 5.5 Deposited 2024-12-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–71（71 aa）	Not recorded	GOL GLYCEROL × 3 NA SODIUM ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；25% PEG3350, 0.1M Bis-Tris pH5.5, 0.25 M AmS	Resolution 1.60 Å R-free 0.225
9HXO A01 mAbs bound to cobratoxin at pH 6.0 Deposited 2025-01-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–71（71 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；25% PEG3350, 0.1M Bis-Tris pH 6.0, 0.3 M Ammonium Sulphate	Resolution 1.49 Å R-free 0.248
9HXO A01 mAbs bound to cobratoxin at pH 6.0 Deposited 2025-01-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–71（71 aa）	Not recorded	GOL GLYCEROL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；25% PEG3350, 0.1M Bis-Tris pH 6.0, 0.3 M Ammonium Sulphate	Resolution 1.49 Å R-free 0.248

12 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	3L21_NAJKA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain V； PDBConstruct 1–71； UniProt 1–71 Author chain X； PDBConstruct 1–71； UniProt 1–71 Author chain Y； PDBConstruct 1–71； UniProt 1–71 Author chain Z； PDBConstruct 1–71； UniProt 1–71

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	9gcn
Deposition date deposition_date	2024-08-02
Structure title title	Co-crystal VHH (TPL1158_01_C09) - alpha-cobratoxin (Naja kaouthia)
Keywords keywords	nanobody, VHH, atibody, antitoxin, toxin, snake toxin, antivenom, neutralising, neutralizing; 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	30.53 Å
Radius of gyration Rg (electron density) rg_electron	29.78 Å
Forward intensity I(0) i0	124270000.00
Molecular weight molecular_weight	82790.0 kDa
Excluded volume excluded_volume	101520 Å³
Envelope volume envelope_volume	142110 Å³
Hydration-shell volume shell_volume	40468 Å³
Envelope diameter envelope_diameter	108.5 Å
Shell Rg shell_rg	36.42 Å
Envelope Rg envelope_rg	29.07 Å
Shape Rg shape_rg	29.74 Å
Total Rg total_rg	30.50 Å
Total atoms total_atoms	11296
Residues n_residues	712
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	103.0 Å
Rg (real space) rg_real	30.46 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	1.2430e+08
I(0) uncertainty (real space) i0_real_error	2.0740e+06
Rg (reciprocal space) rg_reciprocal	30.49 Å
I(0) (reciprocal space) i0_reciprocal	124300000.0000
Solution quality estimate total_estimate	0.8562
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.6 Å
Skewness Skewness skewness	0.347
Kurtosis Kurtosis kurtosis	0.045
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8247000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.867

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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	Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)
Molecular weight formula_weight	13637.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,A,B,C
Atom count atom_count	11297

QVQLQESGGGLVQPGGSLRLSCAASGDIGGLKQMGWYRQAPGHQRELVAVKRNENEANYTESVKGRFTISRDNARKMVYLQMNSLKPEDTAVYYCNAVVGNWYTSGYYEDTYWGQGTQVTVSS

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Alpha-cobratoxin
Molecular weight formula_weight	7842.1 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,V,X,Z

IRCFITPDITSKDCPNGHVCYTKTWCDAFCSIRGKRVDLGCAATCPTVKTGVDIQCCSTDNCNPFPTRKRP

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	65.370 Å
Unit-cell length b length_b	86.010 Å
Unit-cell length c length_c	75.920 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	37.820 Å
R factor r_factor	0.2435
R_work r_work	0.2382
R_free r_free	0.2918

fit	/app/data/saxs_computation/gc/9gcn/9gcn.fit
pddf	/app/data/pr_computation/gc/9gcn/9gcn.pr.out
profile	/app/data/saxs_computation/gc/9gcn/9gcn.dat

Co-crystal VHH (TPL1158_01_C09) - alpha-cobratoxin (Naja kaouthia)

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

Alpha-cobratoxin

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)