Crystal structure of an anti-ssdna antigen-binding fragment (Fab) bound to 4-(2-HYDROXYETHYL)PIPERAZINE-1-ethanesulfonic acid (hepes)

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).

Ligands and binding sites

• SO4 · Sulfate ion · ion · 9 copies · chains L, H, A, B
• GOL · Glycerol · additive · 16 copies · chains L, A, H, B
• 1PE · Pentaethylene glycol · additive · 4 copies · chains L, H, B
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains L, H, A, B
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains L, H

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–B · 1768 Ų buried · 15 hydrogen bonds · protein-protein
• L–H · 1756 Ų buried · 15 hydrogen bonds · protein-protein
• L–A · 240 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

• 1P7K · Crystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to… · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

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• Every structure of UniProt Q8VCP0
• Every structure of UniProt Q9JL75
• Elsewhere: RCSB PDB 1P7K · PDBe 1P7K · UniProt Q8VCP0 · UniProt Q9JL75