› 4rn5

X-ray diffraction
1.73Å resolution

B1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site

Released:
DOI: 10.2210/pdb4rn5/pdb
PDB entry 4rn5 coloured by chain, front view.
PDB entry 4rn5 coloured by chain, side view.
PDB entry 4rn5 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Allerston CK, Yelland TS, Jarvis A, Jenkins K, Winfield N, Cheng L, Jia H, Zachary I, Selwood DL, Djordjevic S

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 Chain: A
Molecule details ›
Chain: A
Length: 158 amino acids
Theoretical weight: 17.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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

3 bound ligands:
Ligand ACT 1 x ACT
Ligand ZN 2 x ZN
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P41212
Unit cell:
a: 62.839Å b: 62.839Å c: 87.918Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.201
Expression system: Escherichia coli

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