9fyt

mAbs in complex with cobratoxin at pH 4.5

Method: X-RAY DIFFRACTION Dmax: 102.1 Å Quality: GOOD

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

Alpha-cobratoxin

Naja kaouthia

UniProt P01391

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–71 Chain B; UniProt 1–71 Not recorded Light chain scFv A01 × 2 heavy chain scFv Ao1 × 2 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

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.

12 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 3L21_NAJKA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–71; UniProt 1–71 Author chain B; 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.

SAXS scattering curve SAXS Profile

SAXS profile for 9fyt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9fyt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9fyt
Deposition date deposition_date2024-07-03
Structure title titlemAbs in complex with cobratoxin at pH 4.5
Keywords keywordsmAbs, cobratoxin, antibody:toxin complex, TOXIN; TOXIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.59
Radius of gyration Rg (electron density) rg_electron28.18
Forward intensity I(0) i084851500.00
Molecular weight molecular_weight69105.0 kDa
Excluded volume excluded_volume84998 ų
Envelope volume envelope_volume105380 ų
Hydration-shell volume shell_volume31654 ų
Envelope diameter envelope_diameter106.4
Shell Rg shell_rg34.84
Envelope Rg envelope_rg28.56
Shape Rg shape_rg28.16
Total Rg total_rg28.89
Total atoms total_atoms9401
Residues n_residues592
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax102.1
Rg (real space) rg_real28.58
Rg uncertainty (real space) rg_real_error0.84
I(0) (real space) i0_real8.4850e+07
I(0) uncertainty (real space) i0_real_error1.3160e+06
Rg (reciprocal space) rg_reciprocal28.59
I(0) (reciprocal space) i0_reciprocal84850000.0000
Solution quality estimate total_estimate0.8621
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.6
Skewness Skewness skewness0.313
Kurtosis Kurtosis kurtosis-0.398
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12440000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.891; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)