5mri

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 18

Method: X-RAY DIFFRACTION Dmax: 94.8 Å Quality: GOOD

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 78–756 Not recorded beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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 × 1 Q9Y ~{N}-methyl-3-(3-methylbutyl)-5-oxidanyl-1,2,3-triazole-4-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.3;292 K;0.1 M HEPES-Tris pH 7.3 0.4 M Sodium malonate 6 % (V/V) glycerol 26 % (w/V) PEG 3350 Resolution 2.00 Å R-free 0.219

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 1–679; UniProt 78–756

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 5mri

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5mri
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5mri
Deposition date deposition_date2016-12-23
Structure title titleCrystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 18
Keywords keywordsVps10p, Receptor, Sortilin, signaling protein; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.71
Radius of gyration Rg (electron density) rg_electron27.65
Forward intensity I(0) i095205600.00
Molecular weight molecular_weight75431.0 kDa
Excluded volume excluded_volume93788 ų
Envelope volume envelope_volume121810 ų
Hydration-shell volume shell_volume35916 ų
Envelope diameter envelope_diameter102.1
Shell Rg shell_rg35.89
Envelope Rg envelope_rg27.44
Shape Rg shape_rg27.62
Total Rg total_rg28.56
Total atoms total_atoms5308
Residues n_residues662
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 dmax94.8
Rg (real space) rg_real28.57
Rg uncertainty (real space) rg_real_error0.83
I(0) (real space) i0_real9.5210e+07
I(0) uncertainty (real space) i0_real_error1.6460e+06
Rg (reciprocal space) rg_reciprocal28.63
I(0) (reciprocal space) i0_reciprocal95210000.0000
Solution quality estimate total_estimate0.8877
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary93.1
Skewness Skewness skewness0.126
Kurtosis Kurtosis kurtosis-0.455
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16520000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.990

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5mriA02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology70 — Complement Module; domain 1
Homologous superfamily homologous superfamily80 — Sortilin Vps10-D, 10CC-a domain
Domain ID domain_id5mriA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily270

8. Citations (1)

9. Files and Curves (10)