S25-23 Fab in complex with chlamydiaceae lps (crystal form 2)

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).

Ligands and binding sites

• GP1 · 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains L, B
• Z9M · 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose · ligand · 2 copies · chains H, A
• KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 6 copies · chains H, L, A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, A
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains H
• NO3 · Nitrate ion · ion · chains B

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

Pockets

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

Interfaces

6 interfaces between chains.

• A–B · 2006 Ų buried · 16 hydrogen bonds · protein-protein
• H–L · 1978 Ų buried · 19 hydrogen bonds · protein-protein
• H–A · 845 Ų buried · 8 hydrogen bonds · protein-protein
• A–L · 106 Ų buried · 1 hydrogen bond · protein-protein
• H–B · 100 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization).

Compared structures

• 6C5K · S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 2) · the same entry in another collection · chain H against H, 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 Q99LC4
• Every structure of UniProt A0A0F7R5U8
• Elsewhere: RCSB PDB 6C5K · PDBe 6C5K · UniProt Q99LC4 · UniProt A0A0F7R5U8