› 5t89

X-ray diffraction
4Å resolution

Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6

Released:
DOI: 10.2210/pdb5t89/pdb
PDB entry 5t89 coloured by chain, front view.
PDB entry 5t89 coloured by chain, side view.
PDB entry 5t89 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the Full-length VEGFR-1 Extracellular Domain in Complex with VEGF-A.
Markovic-Mueller S, Stuttfeld E, Asthana M, Weinert T, Bliven S, Goldie KN, Kisko K, Capitani G, Ballmer-Hofer K
Structure 25 341-352 (2017)
PMID: 28111021

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-538026 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
N-VEGF Chains: V, W
Molecule details ›
Chains: V, W
Length: 131 amino acids
Theoretical weight: 15.2 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P15692 (Residues: 207-321; Coverage: 29%)
  • Best match: P15692-9 (Residues: 27-147)
Gene names: VEGF, VEGFA
Sequence domains: PDGF/VEGF domain
Structure domains: Cystine-knot cytokines
Vascular endothelial growth factor receptor 1 Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 646 amino acids
Theoretical weight: 73.37 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P17948 (Residues: 27-656; Coverage: 48%)
Gene names: FLT, FLT1, FRT, VEGFR1
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 19 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2
Unit cell:
a: 166.71Å b: 123.09Å c: 167.37Å
α: 90° β: 109.56° γ: 90°
R-values:
R R work R free
0.286 0.285 0.315
Expression systems:
  • Komagataella pastoris
  • Spodoptera frugiperda

Quick links

Citations

10 review citations

Molecular Pharmacology of VEGF-A Isoforms: Binding and Signalling at VEGFR2.
Peach et al. (2018)
9 more

26 mentions without citation

Positive and Negative Regulation of Angiogenesis by Soluble Vascular Endothelial Growth Factor Receptor-1.
Failla et al. (2018)
25 more