Crystal structure of monoz-biotin-avidin complex

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).

Ligands and binding sites

• VHI · 5-{(3aS,4S,6aR)-1-[(benzyloxy)carbonyl]-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl}pentanoic acid · ligand · 4 copies · chains A, C, B, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• C–D · 1951 Ų buried · 37 hydrogen bonds · protein-protein
• A–B · 1946 Ų buried · 32 hydrogen bonds · protein-protein
• B–D · 620 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 616 Ų buried · 4 hydrogen bonds · protein-protein
• A–D · 160 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

• 3VHI · Crystal structure of monoZ-biotin-avidin complex · the same entry in another collection · chain D against D, TM-score 1.00
• P02701 · AlphaFold monomer V2.0 prediction for avidin (P02701) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P02701
• Elsewhere: RCSB PDB 3VHI · PDBe 3VHI · UniProt P02701