8z2v

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

Method: X-RAY DIFFRACTION Dmax: 94.6 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 of antibody 5E1 × 1 Light chain of antibody 5E1 × 1 CL CHLORIDE ION × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293.15 K;200mM MgCl2, 20% PEG 3350 Resolution 1.89 Å R-free 0.225

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 8z2v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8z2v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8z2v
Deposition date deposition_date2024-04-13
最后修订 last_revision2025-04-16
Structure title titleCrystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A with 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_guinier28.89
Radius of gyration Rg (electron density) rg_electron28.54
Forward intensity I(0) i066141500.00
Molecular weight molecular_weight63570.0 kDa
Excluded volume excluded_volume79223 ų
Envelope volume envelope_volume97760 ų
Hydration-shell volume shell_volume29890 ų
Envelope diameter envelope_diameter99.9
Shell Rg shell_rg34.66
Envelope Rg envelope_rg28.33
Shape Rg shape_rg28.49
Total Rg total_rg29.24
Total atoms total_atoms4473
Residues n_residues574
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 dmax94.6
Rg (real space) rg_real29.03
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real6.6140e+07
I(0) uncertainty (real space) i0_real_error9.2640e+05
Rg (reciprocal space) rg_reciprocal28.97
I(0) (reciprocal space) i0_reciprocal66140000.0000
Solution quality estimate total_estimate0.8642
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.2
Skewness Skewness skewness0.484
Kurtosis Kurtosis kurtosis-0.285
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12870000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.716

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)