Crystal structure of cyanovirin-N complexed to oligomannose-9 (man-9)

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 57% strand (DSSP).

Ligands and binding sites

• MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains B
• MG · Magnesium ion · metal · chains A, B
• NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3315 Ų buried · 65 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 3GXZ · Crystal structure of cyanovirin-n complexed to oligomannose-9 (man-9) · the same entry in another collection · chain A against A, TM-score 1.00
• P81180 · AlphaFold monomer V2.0 prediction for cyanovirin-N (P81180) · a predicted model of the same protein · chain B against A, TM-score 0.49

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P81180
• Elsewhere: RCSB PDB 3GXZ · PDBe 3GXZ · UniProt P81180