› 8ivw

X-ray diffraction
3.2Å resolution

Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment

Released:
DOI: 10.2210/pdb8ivw/pdb
Model geometry
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PDB entry 8ivw coloured by chain, front view.
PDB entry 8ivw coloured by chain, side view.
PDB entry 8ivw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Inhibition of VEGF binding to neuropilin-2 enhances chemosensitivity and inhibits metastasis in triple-negative breast cancer.
Xu Z, Goel HL, Burkart C, Burman L, Chong YE, Barber AG, Geng Y, Zhai L, Wang M, Kumar A, Menefee A, Polizzi C, Eide L, Rauch K, Rahman J, Hamel K, Fogassy Z, Klopp-Savino S, Paz S, Zhang M, Cubitt A, Nangle LA, Mercurio AM
Sci Transl Med 15 eadf1128 (2023)
PMID: 37134152

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-224893 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Neuropilin-2 Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 583 amino acids
Theoretical weight: 65.95 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O60462 (Residues: 25-595; Coverage: 63%)
Gene names: NRP2, VEGF165R2
Sequence domains:
Heavy chian of antibody 10V8 Fab fragment Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 228 amino acids
Theoretical weight: 24.7 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Light chain of antibody 10V8 Fab fragment Chains: C, F, I, L

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P21
Unit cell:
a: 70.424Å b: 225.164Å c: 142.996Å
α: 90° β: 91.3° γ: 90°
R-values:
R R work R free
0.25 0.248 0.294
Expression system: Homo sapiens

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Citations

3 review citations

Vascular Endothelial Growth Factor-D (VEGF-D): An Angiogenesis Bypass in Malignant Tumors.
Bokhari et al. (2023)
2 more

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