› 5dn2

X-ray diffraction
1.95Å resolution

Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A

Released:
DOI: 10.2210/pdb5dn2/pdb
PDB entry 5dn2 coloured by chain, front view.
PDB entry 5dn2 coloured by chain, side view.
PDB entry 5dn2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket.
Tsai YC, Fotinou C, Rana R, Yelland T, Frankel P, Zachary I, Djordjevic S
FEBS J 283 1921-34 (2016)
PMID: 26991001

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-129977 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Neuropilin-2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 156 amino acids
Theoretical weight: 17.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: O60462 (Residues: 275-429; Coverage: 17%)
Gene names: NRP2, VEGF165R2
Sequence domains: F5/8 type C domain
Structure domains: Galactose-binding domain-like
N-VEGF Chains: E, F, G
Molecule details ›
Chains: E, F, G
Length: 28 amino acids
Theoretical weight: 3.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P15692 (Residues: 368-395; Coverage: 7%)
Gene names: VEGF, VEGFA

Ligands and Environments

2 bound ligands:
Ligand DIO 2 x DIO
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2221
Unit cell:
a: 110.25Å b: 139.52Å c: 106.04Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.234
Expression system: Escherichia coli K-12

Quick links

Citations

2 review citations

Neuropilins: C-end rule peptides and their association with nociception and COVID-19.
Jobe et al. (2021)
1 more

9 mentions without citation

Neuropilin 1 and Neuropilin 2 gene invalidation or pharmacological inhibition reveals their relevance for the treatment of metastatic renal cell carcinoma.
Dumond et al. (2021)
8 more