Semet structure of a novel carbohydrate binding module from glycoside hydrolase family 9 (CEL9A) from ruminococcus flavefaciens fd-1 in the orthorhombic form

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 51% strand (DSSP).

Ligands and binding sites

• HHD · (3S)-3-hydroxyheptanedioic acid · ligand · chains A, B, C
• CA · Calcium ion · metal · chains B
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C
• 2PE · Nonaethylene glycol · additive · chains A
• P6G · Hexaethylene glycol · additive · chains A
• EDO · 1,2-ethanediol · additive · chains A
• GOL · Glycerol · additive · chains B
• PG4 · Tetraethylene glycol · additive · chains C

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–C · 307 Ų buried · 3 hydrogen bonds · protein-protein
• A–B · 295 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 290 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

• 4D3L · SeMet structure of a novel carbohydrate binding module from glycoside hydrolase family 9… · the same entry in another collection · chain A against A, 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
• Elsewhere: RCSB PDB 4D3L · PDBe 4D3L