Crystal structure of scfv-SM3 in complex with apd-cgalnac-rp

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 52% strand (DSSP).

Ligands and binding sites

• A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains H, P
• EDO · 1,2-ethanediol · additive · 4 copies · chains H

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• H–P · 440 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 glycan (disulfide, glycosylation).

Compared structures

• 5A2L · Crystal structure of scFv-SM3 in complex with APD-CGalNAc-RP · the same entry in another collection · chain H against H, TM-score 1.00
• P01801 · AlphaFold monomer V2.0 prediction for ig heavy chain V-III region J606 (P01801) · a predicted model of the same protein · chain H against A, TM-score 0.50
• P01727 · AlphaFold monomer V2.0 prediction for ig lambda-1 chain V region S43 (P01727) · a predicted model of the same protein · chain H against A, TM-score 0.48

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 P01801
• Every structure of UniProt P01727
• Elsewhere: RCSB PDB 5A2L · PDBe 5A2L · UniProt P01801 · UniProt P01727