› 9d77

X-ray diffraction
3.4Å resolution

Crystal form of Netrin-1 mimics nanotubes

Released:
DOI: 10.2210/pdb9d77/pdb
PDB entry 9d77 coloured by chain, front view.
PDB entry 9d77 coloured by chain, side view.
PDB entry 9d77 coloured by chain, top view.
Source organism: Gallus gallus
Entry authors: Meier M, Krahn NJ, McDougall MD, Rafiei F, Koch M, Stetefeld J

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187452 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Netrin-1 Chain: A
Molecule details ›
Chain: A
Length: 443 amino acids
Theoretical weight: 49.58 KDa
Source organism: Gallus gallus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q90922 (Residues: 26-458; Coverage: 75%)
Gene name: NTN1
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand NAG 1 x NAG
Ligand CA 1 x CA
Ligand CL 1 x CL
Ligand MPD 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P6
Unit cell:
a: 189.26Å b: 189.26Å c: 45.88Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.3 0.297 0.335
Expression system: Homo sapiens

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