4nt5

Crystal structure of human von Willebrand factor CTCK domain

Method: X-RAY DIFFRACTION Dmax: 67.5 Å Quality: GOOD

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

von Willebrand factor

Homo sapiens

UniProt P04275

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2721–2813 Fragment:C-terminal cystine knot domain, unp residues 2721-2813 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.3;293 K;1.3 M Lithium Sulfate, 0.1 M Bicine, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.28 Å R-free 0.248

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.

46 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VWF_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 15–107; UniProt 2721–2813

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 4nt5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4nt5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4nt5
Deposition date deposition_date2013-12-01
Structure title titleCrystal structure of human von Willebrand factor CTCK domain
Keywords keywordscystine knot, dimerization of VWF, 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_guinier19.72
Radius of gyration Rg (electron density) rg_electron19.28
Forward intensity I(0) i03204410.00
Molecular weight molecular_weight11088.0 kDa
Excluded volume excluded_volume13079 ų
Envelope volume envelope_volume18977 ų
Hydration-shell volume shell_volume9321 ų
Envelope diameter envelope_diameter66.1
Shell Rg shell_rg23.56
Envelope Rg envelope_rg19.05
Shape Rg shape_rg19.32
Total Rg total_rg19.91
Total atoms total_atoms751
Residues n_residues93
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 dmax67.5
Rg (real space) rg_real19.96
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real3.2040e+06
I(0) uncertainty (real space) i0_real_error4.1870e+04
Rg (reciprocal space) rg_reciprocal19.92
I(0) (reciprocal space) i0_reciprocal3204000.0000
Solution quality estimate total_estimate0.8263
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.2
Skewness Skewness skewness0.422
Kurtosis Kurtosis kurtosis-0.530
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha233700.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.396; Smooth: 0.940

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)