| Title | Crystal structure of putative glucoamylase (YP_210071.1) from Bacteroides fragilis NCTC 9343 at 2.12 A resolution. | | Site | JCSG | | PDB Id | | Target Id | 390129 | | Molecular Characteristics | | Source | Bacteroides fragilis nctc 9343 | | Alias Ids | YP_210071.1 | Molecular Weight | 48501.26 Da. | | Residues | 429 | Isoelectric Point | 5.82 | | Sequence | vackpkekpssatsltddalmdtvqrrtfnyfwdaaepnsglareryhmdgeypaggpeivtsggsgfgi mailagidrgyvsreeglrrmekivgflekadrfkgayphwwngetghvqpfgqkdnggdlvetaflmq gllavhqyyaegsaeekklagridklwrevdwnwyrhggqnvlywhwspeygwemnfpvhgyneclimy ilaaaspthgvpaavyhegwaqngaivsphkvegielhlryqggeagplfwaqysflgldpvglkdeyc psyfnemrnltlvnreycirnpkhykgygpdcwgltasysvdgyaahgplerddrgvisptaalssivy tpdqslqvmhhlyemgdkvfgpygfydafsetadwypkrylaidqgpiavmienyrtgllwklfmshpd vqnglkklgfnvkk | | | BLAST FFAS |
| Structure Determination | | Method | XRAY | Chains | 4 | | Resolution (Å) | 2.12 | Rfree | 0.213 | | Matthews' coefficent | 2.35 | Rfactor | 0.158 | | Waters | 1248 | Solvent Content | 47.69 |
| Ligand Information | | Ligands | EDO (1,2-ETHANEDIOL) x 84 | | Metals | K (POTASSIUM) x 5;CL (CHLORIDE) x 1 | | |
Protein Summary
390129 is a member of COG5368 family. The structure (Figure 1) has a alpha/alpha toroid fold and is similar to 1ayx (Z=19.9), 1glm (Z=19.4), 1gah, 1dog, 1agm, 3gly etc. The sequence similarities between 390129 and these structural homologs are usually less than 10%. Most of these structural homologs are glucoamylases which are involved in breaking down complex sugars (e.g. starch). The biological relevant state is likely monomeric. The putative active site is located at the center of the toroid with a well defined large cavity (Figure 2).
Figure 1. The monomer of 390129
Figure 2. The putative active site on the surface 390129
Ligand Summary
