› 2qqk

X-ray diffraction
2.75Å resolution

Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab

Released:
DOI: 10.2210/pdb2qqk/pdb
PDB entry 2qqk coloured by chain, front view.
PDB entry 2qqk coloured by chain, side view.
PDB entry 2qqk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding.
Appleton BA, Wu P, Maloney J, Yin J, Liang WC, Stawicki S, Mortara K, Bowman KK, Elliott JM, Desmarais W, Bazan JF, Bagri A, Tessier-Lavigne M, Koch AW, Wu Y, Watts RJ, Wiesmann C
EMBO J 26 4902-12 (2007)
PMID: 17989695

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero hexamer
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208108 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Neuropilin-2 Chain: A
Molecule details ›
Chain: A
Length: 579 amino acids
Theoretical weight: 65.39 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O60462 (Residues: 23-595; Coverage: 63%)
Gene names: NRP2, VEGF165R2
Sequence domains:
Structure domains:
Antibody Heavy Chain Chain: H
Molecule details ›
Chain: H
Length: 231 amino acids
Theoretical weight: 24.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Antibody Light Chain Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 23.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: C2
Unit cell:
a: 148.277Å b: 105.873Å c: 92.4Å
α: 90° β: 98.83° γ: 90°
R-values:
R R work R free
0.189 0.186 0.243
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

54 review citations

Role and therapeutic potential of VEGF in the nervous system.
Ruiz de Almodovar et al. (2009)
53 more

13 mentions without citation

Neuropilin Functions as an Essential Cell Surface Receptor.
Guo et al. (2015)
12 more