9r18

Structure of Sortilin ECD in complex with TNFa-targeting SORTAC

Method: X-RAY DIFFRACTION Dmax: 94.5 Å Quality: REASONABLE

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

Sortilin

Homo sapiens

UniProt Q99523

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 Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–756 Mutation:V650M 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1JCL (2~{S})-2-[[6-[3-[8-[2-[(2~{R})-4-[5-[1-[(2-cyanopyridin-3-yl)methyl]-2,2-dimethyl-3-oxidanylidene-pyrrolo[2,3-b]pyridin-6-yl]pyrimidin-2-yl]-2-methyl-piperazin-1-yl]-2-oxidanylidene-ethoxy]octylcarbamoyl]phenoxy]pyridin-3-yl]carbonylamino]-5,5-dimethyl-hexanoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;292.15 K;22 % PEG6000, 1.1 M NaCl, 8% glycerol, 50 mM HEPES pH 8.0 Resolution 2.80 Å R-free 0.253

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.

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

View Construct and Data Evidence
UniProt name SORT_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–756; UniProt 1–756

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 9r18

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9r18
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9r18
Deposition date deposition_date2025-04-25
Structure title titleStructure of Sortilin ECD in complex with TNFa-targeting SORTAC
Keywords keywordsLysosome sorting receptor, Targeted protein degradation, SORtilin-based lysosome TArgeting Chimeras (SORTACs), PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.83
Radius of gyration Rg (electron density) rg_electron27.73
Forward intensity I(0) i094156600.00
Molecular weight molecular_weight75627.0 kDa
Excluded volume excluded_volume94315 ų
Envelope volume envelope_volume124160 ų
Hydration-shell volume shell_volume36477 ų
Envelope diameter envelope_diameter101.4
Shell Rg shell_rg35.93
Envelope Rg envelope_rg27.54
Shape Rg shape_rg27.73
Total Rg total_rg28.56
Total atoms total_atoms10447
Residues n_residues658
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 dmax94.5
Rg (real space) rg_real28.68
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real9.4160e+07
I(0) uncertainty (real space) i0_real_error1.2510e+06
Rg (reciprocal space) rg_reciprocal28.75
I(0) (reciprocal space) i0_reciprocal94160000.0000
Solution quality estimate total_estimate0.6935
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.5
Skewness Skewness skewness0.114
Kurtosis Kurtosis kurtosis-0.452
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17580000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 0.156; Positv: 1.000; Valcen: 1.000; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)