4bsj

Crystal structure of VEGFR-3 extracellular domains D4-5

Method: X-RAY DIFFRACTION Dmax: 95.3 Å Quality: REASONABLE

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

VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3

HOMO SAPIENS

UniProt P35916

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 330–553 Fragment:EXTRACELLULAR DOMAINS 4 AND 5 (D4-5), RESIDUES 330-553 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 298 K, PHOSPHATE BUFFER 0.1 M, PH 7.5 - 8.5, PEG 400 25%. Resolution 2.50 Å R-free 0.253
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 330–553 Fragment:EXTRACELLULAR DOMAINS 4 AND 5 (D4-5), RESIDUES 330-553 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 298 K, PHOSPHATE BUFFER 0.1 M, PH 7.5 - 8.5, PEG 400 25%. Resolution 2.50 Å R-free 0.253

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 VGFR3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–226; UniProt 330–553

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 4bsj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4bsj
Deposition date deposition_date2013-06-10
Structure title titleCrystal structure of VEGFR-3 extracellular domains D4-5
Keywords keywordsTRANSFERASE, LYMPHANGIOGENESIS, ANGIOGENESIS, VASCULAR, IG DOMAIN, GLYCOPROTEIN, RECEPTOR TYROSINE KINASE, DIMERIZATION; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.25
Radius of gyration Rg (electron density) rg_electron26.26
Forward intensity I(0) i09805350.00
Molecular weight molecular_weight24090.0 kDa
Excluded volume excluded_volume30384 ų
Envelope volume envelope_volume39705 ų
Hydration-shell volume shell_volume14637 ų
Envelope diameter envelope_diameter98.0
Shell Rg shell_rg29.22
Envelope Rg envelope_rg26.61
Shape Rg shape_rg26.29
Total Rg total_rg26.55
Total atoms total_atoms1701
Residues n_residues213
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 dmax95.3
Rg (real space) rg_real26.76
Rg uncertainty (real space) rg_real_error1.31
I(0) (real space) i0_real9.8050e+06
I(0) uncertainty (real space) i0_real_error1.6810e+05
Rg (reciprocal space) rg_reciprocal26.60
I(0) (reciprocal space) i0_reciprocal9804000.0000
Solution quality estimate total_estimate0.7025
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.1
Skewness Skewness skewness0.623
Kurtosis Kurtosis kurtosis-0.427
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1440000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.349; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.098; Smooth: 0.984

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4bsjA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4bsjA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)