4rly

Crystal Structure of AnkB Ankyrin Repeats (R1-R9) in Complex with Nav1.2 Ankyrin Binding Domain

Method: X-RAY DIFFRACTION Dmax: 88.4 Å Quality: GOOD

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

Nav1.2 - AnkB chimera

Homo sapiens

UniProt A9JQD3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 74–92 Not recorded SO4 SULFATE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;289 K;1.8 M ammonium sulfate, 6-8% dioxane, and 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.50 Å R-free 0.238
2 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 74–92 Not recorded SO4 SULFATE ION × 14 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;289 K;1.8 M ammonium sulfate, 6-8% dioxane, and 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.50 Å R-free 0.238

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A9JQD3_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–21; UniProt 74–92

Nav1.2 - AnkB chimera

Homo sapiens

UniProt Q01484

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 28–318 Not recorded SO4 SULFATE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;289 K;1.8 M ammonium sulfate, 6-8% dioxane, and 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.50 Å R-free 0.238
2 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 28–318 Not recorded SO4 SULFATE ION × 14 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;289 K;1.8 M ammonium sulfate, 6-8% dioxane, and 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.50 Å R-free 0.238

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.

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

View Construct and Data Evidence
UniProt name ANK2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 30–320; UniProt 28–318

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 4rly

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4rly
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4rly
Deposition date deposition_date2014-10-18
Structure title titleCrystal Structure of AnkB Ankyrin Repeats (R1-R9) in Complex with Nav1.2 Ankyrin Binding Domain
Keywords keywordsANK Repeat, Protein-protein interaction, Structural protein; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.66
Radius of gyration Rg (electron density) rg_electron25.41
Forward intensity I(0) i020862000.00
Molecular weight molecular_weight32838.0 kDa
Excluded volume excluded_volume40272 ų
Envelope volume envelope_volume50225 ų
Hydration-shell volume shell_volume18510 ų
Envelope diameter envelope_diameter89.7
Shell Rg shell_rg29.76
Envelope Rg envelope_rg25.79
Shape Rg shape_rg25.42
Total Rg total_rg25.88
Total atoms total_atoms2297
Residues n_residues308
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 dmax88.4
Rg (real space) rg_real25.99
Rg uncertainty (real space) rg_real_error0.84
I(0) (real space) i0_real2.0860e+07
I(0) uncertainty (real space) i0_real_error2.9350e+05
Rg (reciprocal space) rg_reciprocal25.89
I(0) (reciprocal space) i0_reciprocal20860000.0000
Solution quality estimate total_estimate0.7846
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.4
Skewness Skewness skewness0.602
Kurtosis Kurtosis kurtosis-0.314
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8496000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.594; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.529; Smooth: 0.897

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4rlyA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily20 — Ankyrin repeat-containing domain

8. Citations (1)

9. Files and Curves (10)