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Table 3 Dataset used in comparison of ligated and unligated pairs

From: How accurate and statistically robust are catalytic site predictions based on closeness centrality?

Enzyme1 Ligated vs. unligated2 Protein length SCOP class Correl3 RMSD (Å)4
4-oxalocrotonate tautomerase (1BJP, 4OTB) 1, 2, 0 59 α + β 0.985 0.4
Ribonuclease A (1RBN, 1RSM) 0, 2, 2 124 α + β 0.984 0.6
Xylanase II (1BVV, 1XNB) 1, 1, 0 185 β 0.997 0.2
Trpysin (1A0J, 1UTK) 1, 2, 0 245 β 0.983 1.1
Aminopeptidase (1IGB, 1AMP) 1, 0, 0 291 α/β 0.992 0.6
Phospholipase C (1AOD, 2PLC) 3, 0, 2 294 α/β 0.992 0.2
Deacetoxycephalosporin C synthase (1W2N, 1W28) 0, 1, 0 298 β 0.980 0.5
Chorismate mutase (3CSM, 2CSM) 2, 2, 0 300 α 0.955 1.9
Alginate lyase A1-III (1HV6, 1QAZ) 2, 0, 1 354 α 0.995 0.1
tRNA-guanine transglycosylase (1R5Y, 1PUD) 1, 0, 0 382 α/β 0.814 0.5
Nitric oxide synthase oxygenase (1M9R, 3NOS) 2, 2, 0 480 α + β 0.992 0.2
Luciferase (1BA3, 1LCI) 3, 1, 0 544 Multi. 0.948 0.5
Class I alpha-1;2-mannosidase (1G6I, 1DL2) 1, 3, 0 549 α 0.996 0.1
Average 3 0.970 0.5
Standard deviation 0.049 0.5
Correlation (Correl vs. RMSD) -0.17
  1. 1 SCOP protein name for each pair examined. The ligated and unligated PDB id's, respectively, are provided in parentheses. 2 The three values (ligated, unligated, tie) tabulate the number of catalytic residues with higher rank ordering between the structural pair. 3 Linear correlation coefficient comparing the CC scores between each structural pair. 4 Pairwise RMSD comparing structure similarity within each pair. Surprisingly, there is no significant correlation between the last two columns.