SAXSdb — 9rit

▼

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

Cytotoxin 1

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 C； UniProt 1–60	Not recorded	Variable Domain of Heavy-Chain only Antibody (VHH) × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.2M Ammonium acetate, 0.1M Sodium acetate, pH 4.6, 30% w/v PEG 4000. 25% (v/v) glycerol as cryoprotection.	Resolution 1.60 Å R-free 0.258
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–60	Not recorded	Variable Domain of Heavy-Chain only Antibody (VHH) × 1 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.2M Ammonium acetate, 0.1M Sodium acetate, pH 4.6, 30% w/v PEG 4000. 25% (v/v) glycerol as cryoprotection.	Resolution 1.60 Å R-free 0.258

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 9RIT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CXN REFINED THREE-DIMENSIONAL SOLUTION STRUCTURE OF A SNAKE CARDIOTOXIN: ANALYSIS OF THE SIDE-CHAIN ORGANISATION SUGGESTS THE EXISTENCE OF A POSSIBLE PHOSPHOLIPID BINDING SITE Deposited 1994-07-08	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 1–60（60 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CXO REFINED THREE-DIMENSIONAL SOLUTION STRUCTURE OF A SNAKE CARDIOTOXIN: ANALYSIS OF THE SIDE-CHAIN ORGANISATION SUGGESTS THE EXISTENCE OF A POSSIBLE PHOSPHOLIPID BINDING SITE Deposited 1994-11-07	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 1–60（60 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1TGX X-RAY STRUCTURE AT 1.55 A OF TOXIN GAMMA, A CARDIOTOXIN FROM NAJA NIGRICOLLIS VENOM. CRYSTAL PACKING REVEALS A MODEL FOR INSERTION INTO MEMBRANES Deposited 1993-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–60（60 aa） Chain B 1–60（60 aa） Chain C 1–60（60 aa）	Not recorded	CL CHLORIDE ION × 28	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å
1TGX X-RAY STRUCTURE AT 1.55 A OF TOXIN GAMMA, A CARDIOTOXIN FROM NAJA NIGRICOLLIS VENOM. CRYSTAL PACKING REVEALS A MODEL FOR INSERTION INTO MEMBRANES Deposited 1993-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–60（60 aa） Chain B 1–60（60 aa） Chain C 1–60（60 aa）	Not recorded	CL CHLORIDE ION × 28	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å
1TGX X-RAY STRUCTURE AT 1.55 A OF TOXIN GAMMA, A CARDIOTOXIN FROM NAJA NIGRICOLLIS VENOM. CRYSTAL PACKING REVEALS A MODEL FOR INSERTION INTO MEMBRANES Deposited 1993-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–60（60 aa） Chain B 1–60（60 aa） Chain C 1–60（60 aa）	Not recorded	CL CHLORIDE ION × 28	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å
1TGX X-RAY STRUCTURE AT 1.55 A OF TOXIN GAMMA, A CARDIOTOXIN FROM NAJA NIGRICOLLIS VENOM. CRYSTAL PACKING REVEALS A MODEL FOR INSERTION INTO MEMBRANES Deposited 1993-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–60（60 aa） Chain B 1–60（60 aa） Chain C 1–60（60 aa）	Not recorded	CL CHLORIDE ION × 28	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å
9BK6 Structure of B10_CYTX binder-complex Deposited 2024-04-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–60（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES pH 6, 0.01 M Zinc chloride, 20% (w/v) PEG 6000 and 10 % (v/v) Ethylene glycol	Resolution 2.00 Å R-free 0.285

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	3SA1_NAJPA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–60； UniProt 1–60 Author chain D； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9rit
Deposition date deposition_date	2025-06-11
Structure title title	Co-crystal of broadly neutralizing biparatopic VHH in complex with cardiotoxin (P01468) Naja pallida
Keywords keywords	nanobody, VHH, antibody, toxin, snake toxin, snake venom, neutralizing, cytotoxin, biparatopic; TOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	24.02 Å
Radius of gyration Rg (electron density) rg_electron	23.19 Å
Forward intensity I(0) i0	28989700.00
Molecular weight molecular_weight	39870.0 kDa
Excluded volume excluded_volume	49378 Å³
Envelope volume envelope_volume	61845 Å³
Hydration-shell volume shell_volume	22944 Å³
Envelope diameter envelope_diameter	83.9 Å
Shell Rg shell_rg	29.44 Å
Envelope Rg envelope_rg	23.17 Å
Shape Rg shape_rg	23.17 Å
Total Rg total_rg	24.07 Å
Total atoms total_atoms	2800
Residues n_residues	356
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	77.8 Å
Rg (real space) rg_real	23.94 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	2.8990e+07
I(0) uncertainty (real space) i0_real_error	4.2640e+05
Rg (reciprocal space) rg_reciprocal	23.96 Å
I(0) (reciprocal space) i0_reciprocal	28990000.0000
Solution quality estimate total_estimate	0.9017
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.6 Å
Skewness Skewness skewness	0.195
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3490000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.983

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Variable Domain of Heavy-Chain only Antibody (VHH)
Molecular weight formula_weight	13832.0 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	3094

QVQLQESGGGLVQAGGSLRLSCAASGRTFSSYAMAWFRQAPGKEREFVASISWNGDSTYYADSVKGRFTISGDNAKNTWYLQMKSLKPEDTAVYYCNTEDEGSGTYYEWGQGTQVTVSSENLYFQ

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	Cytotoxin 1
Molecular weight formula_weight	6838.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	270

▶

8. Citations (1)

▶

Unit-cell length a length_a	41.943 Å
Unit-cell length b length_b	54.905 Å
Unit-cell length c length_c	143.014 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	8

Space group space_group	P 2 2 21
Space-group number int_tables_number	17
Crystal system crystal_system	orthorhombic

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	51.260 Å
R factor r_factor	0.2238
R_work r_work	0.2220
R_free r_free	0.2578

fit	/app/data/saxs_computation/ri/9rit/9rit.fit
pddf	/app/data/pr_computation/ri/9rit/9rit.pr.out
profile	/app/data/saxs_computation/ri/9rit/9rit.dat

Co-crystal of broadly neutralizing biparatopic VHH in complex with cardiotoxin (P01468) Naja pallida

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

Cytotoxin 1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)