Crystal structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a GP41 11MER epitope

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · chains P
• NH2 · Amino group · ion · chains H, P
• IPA · Isopropyl alcohol · additive · 6 copies · chains L, H
• EDO · 1,2-ethanediol · additive · 2 copies · chains H, L

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

Pockets

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

Interfaces

3 interfaces between chains.

• L–H · 2045 Ų buried · 19 hydrogen bonds · protein-protein
• H–P · 459 Ų buried · 11 hydrogen bonds · protein-protein
• L–P · 333 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 modified, 1 covalent (disulfide, alkylation, covalent ligand).

Compared structures

• 1TJH · Crystal Structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a… · the same entry in another collection · chain L against L, TM-score 1.00

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 P04580
• Elsewhere: RCSB PDB 1TJH · PDBe 1TJH · UniProt P04580