› 5dq0

X-ray diffraction
1.8Å resolution

Structure of human neuropilin-2 b1 domain with novel and unique zinc binding site

Released:
DOI: 10.2210/pdb5dq0/pdb
PDB entry 5dq0 coloured by chain, front view.
PDB entry 5dq0 coloured by chain, side view.
PDB entry 5dq0 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Tsai YI, Rana RR, Zachary I, 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-129976 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Neuropilin-2 Chain: A
Molecule details ›
Chain: A
Length: 162 amino acids
Theoretical weight: 18.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60462 (Residues: 275-430; Coverage: 17%)
Gene names: NRP2, VEGF165R2
Sequence domains: F5/8 type C domain
Structure domains: Galactose-binding domain-like

Ligands and Environments

4 bound ligands:
Ligand ZN 3 x ZN
Ligand CL 2 x CL
Ligand EDO 2 x EDO
Ligand MES 1 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: C2221
Unit cell:
a: 99.39Å b: 105.27Å c: 45.75Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.217
Expression system: Escherichia coli

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