2lms

A single GalNAc residue on Threonine-106 modifies the dynamics and the structure of Interferon alpha-2a around the glycosylation site

Method: SOLUTION NMR Dmax: 45.6 Å Quality: GOOD

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

Interferon alpha-2

Homo sapiens

UniProt P01563

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 24–188 Not recorded A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 SOLUTION NMR NMR measurement conditions:pH 3.5;298.15 K;Ionic strength (raw mmCIF value) 25;Pressure ambient NMR sample composition:0.85 mM [U-100% 13C; U-100% 15N] Interferon Alpha-2a (O-glycosylated), 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.87 mM [U-100% 13C; U-100% 15N] Interferon Alpha-2a (O-glycosylated), 100% D2O | 100% D2O Resolution not provided

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.

11 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IFNA2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–166; UniProt 24–188

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 2lms

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2lms
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2lms
Deposition date deposition_date2011-12-12
Structure title titleA single GalNAc residue on Threonine-106 modifies the dynamics and the structure of Interferon alpha-2a around the glycosylation site
Keywords keywordsCYTOKINE, GLYCOPROTEIN, O-GLYCOSYLATION, SIGNALING PROTEIN, TYPE I INTERFERONS, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier16.22
Radius of gyration Rg (electron density) rg_electron16.04
Forward intensity I(0) i02022920000.00
Molecular weight molecular_weight388530.0 kDa
Excluded volume excluded_volume488400 ų
Envelope volume envelope_volume40771 ų
Hydration-shell volume shell_volume18897 ų
Envelope diameter envelope_diameter58.8
Shell Rg shell_rg24.41
Envelope Rg envelope_rg18.21
Shape Rg shape_rg15.99
Total Rg total_rg16.36
Total atoms total_atoms54440
Residues n_residues3300
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 dmax45.6
Rg (real space) rg_real16.11
Rg uncertainty (real space) rg_real_error0.18
I(0) (real space) i0_real2.0230e+09
I(0) uncertainty (real space) i0_real_error1.8500e+07
Rg (reciprocal space) rg_reciprocal16.12
I(0) (reciprocal space) i0_reciprocal2023000000.0000
Solution quality estimate total_estimate0.8532
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.1
Skewness Skewness skewness0.104
Kurtosis Kurtosis kurtosis-0.452
Angular range angular_range— – 0.4900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha639100.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.213

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2lmsa_
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.3 — Interferons/interleukin-10 (IL-10)

CATH v4.4 (1 domains)

Domain ID domain_id2lmsA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)