› 5ijr

X-ray diffraction
1.52Å resolution

X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand.

Released:
DOI: 10.2210/pdb5ijr/pdb
PDB entry 5ijr coloured by chain, front view.
PDB entry 5ijr coloured by chain, side view.
PDB entry 5ijr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Architecture and hydration of the arginine-binding site of neuropilin-1.
Mota F, Fotinou C, Rana RR, Chan AWE, Yelland T, Arooz MT, O'Leary AP, Hutton J, Frankel P, Zachary I, Selwood D, Djordjevic S
OpenAccess logo FEBS J 285 1290-1304 (2018)
PMID: 29430837

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127136 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Neuropilin-1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 156 amino acids
Theoretical weight: 17.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O14786 (Residues: 273-427; Coverage: 17%)
Gene names: NRP, NRP1, VEGF165R
Sequence domains: F5/8 type C domain
Structure domains: Galactose-binding domain-like

Ligands and Environments

2 bound ligands:
Ligand HRG 1 x HRG
Ligand DMS 1 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 40.139Å b: 88.936Å c: 40.962Å
α: 90° β: 96.73° γ: 90°
R-values:
R R work R free
0.183 0.181 0.213
Expression system: Escherichia coli BL21

Quick links

Citations

5 review citations

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

4 mentions without citation

Architecture and hydration of the arginine-binding site of neuropilin-1.
Mota et al. (2018)
3 more