6kzj

Crystal structure of Ankyrin B/NdeL1 complex

Method: X-RAY DIFFRACTION Dmax: 67.0 Å Quality: GOOD

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

Ankyrin-2

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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1499–1570 Not recorded Nuclear distribution protein nudE-like 1 × 2 (Q9ERR1) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.6;289 K;1.9M ammonium sulfate, 0.16M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dehydrate pH 5.6 Resolution 1.50 Å R-free 0.211

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 19 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 5–76; UniProt 1499–1570

Nuclear distribution protein nudE-like 1

Mus musculus

UniProt Q9ERR1

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 B; UniProt 238–284 Chain C; UniProt 238–284 Not recorded Ankyrin-2 × 1 (Q01484) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.6;289 K;1.9M ammonium sulfate, 0.16M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dehydrate pH 5.6 Resolution 1.50 Å R-free 0.211

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NDEL1_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 5–51; UniProt 238–284 Author chain C; PDBConstruct 5–51; UniProt 238–284

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 6kzj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6kzj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6kzj
Deposition date deposition_date2019-09-24
Structure title titleCrystal structure of Ankyrin B/NdeL1 complex
Keywords keywordsPROTEIN TRANSPORT, STRUCTURAL PROTEIN, 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_guinier17.42
Radius of gyration Rg (electron density) rg_electron16.47
Forward intensity I(0) i04682530.00
Molecular weight molecular_weight15685.0 kDa
Excluded volume excluded_volume19781 ų
Envelope volume envelope_volume23807 ų
Hydration-shell volume shell_volume12875 ų
Envelope diameter envelope_diameter65.9
Shell Rg shell_rg21.54
Envelope Rg envelope_rg17.21
Shape Rg shape_rg16.53
Total Rg total_rg17.27
Total atoms total_atoms1100
Residues n_residues150
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 dmax67.0
Rg (real space) rg_real17.47
Rg uncertainty (real space) rg_real_error0.69
I(0) (real space) i0_real4.6830e+06
I(0) uncertainty (real space) i0_real_error6.7340e+04
Rg (reciprocal space) rg_reciprocal17.47
I(0) (reciprocal space) i0_reciprocal4683000.0000
Solution quality estimate total_estimate0.7768
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.8
Skewness Skewness skewness0.481
Kurtosis Kurtosis kurtosis0.051
Angular range angular_range— – 0.4550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1050000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.465; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.699; Smooth: 1.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)