8udz

The Structure of LTBP-49247 Fab Bound to TGFbeta1 Small Latent Complex

Method: X-RAY DIFFRACTION Dmax: 170.4 Å Quality: GOOD

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

Transforming growth factor beta-1 proprotein

Homo sapiens

UniProt P01137

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 6 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 30–390 Chain B; UniProt 30–390 Mutation:C33S, R278A LTBP-49247 Fab Heavy Chain × 2 LTBP-49247 Fab Light Chain × 2 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4;293 K;15% PEG 3350, 12% Tacsimate (pH 4.0), 10 mM Magnesium Chloride Resolution 2.21 Å R-free 0.264

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.

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

View Construct and Data Evidence
UniProt name TGFB1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–361; UniProt 30–390 Author chain B; PDBConstruct 1–361; UniProt 30–390

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 8udz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8udz
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id8udz
Deposition date deposition_date2023-09-29
Structure title titleThe Structure of LTBP-49247 Fab Bound to TGFbeta1 Small Latent Complex
Keywords keywordsGrowth factor, antibody, fibrosis, TGFbeta, SIGNALING PROTEIN, SIGNALING PROTEIN-IMMUNE SYSTEM complex; SIGNALING PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier49.70
Radius of gyration Rg (electron density) rg_electron50.06
Forward intensity I(0) i0369963000.00
Molecular weight molecular_weight157710.0 kDa
Excluded volume excluded_volume196960 ų
Envelope volume envelope_volume296330 ų
Hydration-shell volume shell_volume52058 ų
Envelope diameter envelope_diameter170.4
Shell Rg shell_rg49.64
Envelope Rg envelope_rg49.60
Shape Rg shape_rg50.07
Total Rg total_rg50.02
Total atoms total_atoms11092
Residues n_residues1422
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 dmax170.4
Rg (real space) rg_real50.01
Rg uncertainty (real space) rg_real_error1.98
I(0) (real space) i0_real3.7000e+08
I(0) uncertainty (real space) i0_real_error7.4150e+06
Rg (reciprocal space) rg_reciprocal49.70
I(0) (reciprocal space) i0_reciprocal369800000.0000
Solution quality estimate total_estimate0.8566
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.6
Skewness Skewness skewness0.299
Kurtosis Kurtosis kurtosis-0.709
Angular range angular_range— – 0.1600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22120000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.824; Smooth: 0.756

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)