Molecular Phylogeny and Predicted 3D Structure of Plant beta-D-𝑁-Acetylhexosaminidase

Table 4

Template proteins with similar binding sites searched by COFACTOR.

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Predicted binding sites
1	0.64	3lmyA	0.78	2.19	0.345	0.82	1.55	CP6	178, 204, 207, 261, 330, 404, 430, 432, 433, 494, 496
2	0.45	2gk1G	0.77	2.56	0.300	0.82	1.50	NGT	178, 251, 330, 331, 378, 404, 429, 494, 496
3	0.06	2gjx1	0.78	2.56	0.344	0.82	0.95	Peptide	178, 179, 227, 228, 230, 231, 464, 496, 497, 499, 500, 501, 502, 505, 506

Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1], where a higher score is better site prediction.
BS-score is a measure of local similarity (sequence and structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis; we have observed that a BS-score > 1 reflects a significant local match between the predicted and template binding site.
TM-score is a measure of global structural similarity between query and template protein.
RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
IDEN^a is the percentage sequence identity in the structurally aligned region.
Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues.