› 2xv7

X-ray diffraction
2.9Å resolution

Crystal structure of vascular endothelial growth factor D

Released:
DOI: 10.2210/pdb2xv7/pdb
PDB entry 2xv7 coloured by chain, front view.
PDB entry 2xv7 coloured by chain, side view.
PDB entry 2xv7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural determinants of vascular endothelial growth factor-D receptor binding and specificity.
Leppänen VM, Jeltsch M, Anisimov A, Tvorogov D, Aho K, Kalkkinen N, Toivanen P, Ylä-Herttuala S, Ballmer-Hofer K, Alitalo K
Blood 117 1507-15 (2011)
PMID: 21148085

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129166 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Vascular endothelial growth factor D Chain: A
Molecule details ›
Chain: A
Length: 112 amino acids
Theoretical weight: 12.56 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O43915 (Residues: 92-195; Coverage: 31%)
Gene names: FIGF, VEGFD
Sequence domains: PDGF/VEGF domain
Structure domains: Cystine-knot cytokines

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand MAN 2 x MAN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P6122
Unit cell:
a: 95.72Å b: 95.72Å c: 70.94Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.263 0.255 0.332
Expression system: Spodoptera frugiperda

Quick links

Citations

21 review citations

The lymphatic vasculature in disease.
Alitalo K. (2011)
20 more

7 mentions without citation

A Structural Overview of Vascular Endothelial Growth Factors Pharmacological Ligands: From Macromolecules to Designed Peptidomimetics.
Ye et al. (2021)
6 more