8yyz

Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A in the absence of metals

Method: X-RAY DIFFRACTION Dmax: 93.8 Å Quality: GOOD

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

Sonic hedgehog protein N-product

Homo sapiens

UniProt Q15465

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 29–197 Not recorded Heavy chain antibody 5E1 mutated × 1 Light chain antibody 5E1 × 1 CL CHLORIDE ION × 5 GOL GLYCEROL × 1 IOD IODIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293.15 K;0.2M Ammonium iodide, 20% w/v Polyethylene glycol 3350 Resolution 1.90 Å R-free 0.222

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.

18 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SHH_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–169; UniProt 29–197

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 8yyz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8yyz
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id8yyz
Deposition date deposition_date2024-04-04
最后修订 last_revision2025-04-09
Structure title titleCrystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A in the absence of metals
Keywords keywordsSonic hedgehog protein (SHH), antibody, flexible/fluctuated epitope, affinity improvement, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.90
Radius of gyration Rg (electron density) rg_electron28.49
Forward intensity I(0) i068680500.00
Molecular weight molecular_weight64093.0 kDa
Excluded volume excluded_volume79575 ų
Envelope volume envelope_volume98415 ų
Hydration-shell volume shell_volume30042 ų
Envelope diameter envelope_diameter99.3
Shell Rg shell_rg34.61
Envelope Rg envelope_rg28.28
Shape Rg shape_rg28.43
Total Rg total_rg29.24
Total atoms total_atoms4495
Residues n_residues577
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 dmax93.8
Rg (real space) rg_real29.02
Rg uncertainty (real space) rg_real_error0.72
I(0) (real space) i0_real6.8680e+07
I(0) uncertainty (real space) i0_real_error9.5190e+05
Rg (reciprocal space) rg_reciprocal28.97
I(0) (reciprocal space) i0_reciprocal68680000.0000
Solution quality estimate total_estimate0.8601
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.7
Skewness Skewness skewness0.461
Kurtosis Kurtosis kurtosis-0.313
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12800000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.597

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)