Table 1

Positive results for some additional examples

PDB IDNameChemistryResidues with positive results
1AMQ Aspartate aminotransferase*Transamination[H189, Y225, K258, R266, C191, C192], [Y256], [Y295], [H301]
1CSE Subtilisin CarlsbergPeptide hydrolysis (serine protease)[D32, H64]
1EA5 AcetylcholinesteraseEster hydrolysis[Y130, E199, E327, H440, D392], [Y148], [H398], [H425]
1HKA 6–Hydroxymethyl–7,8–dihydropterin pyrophosphate kinase*Kinase[D97, H115]
1OPY 3-Keto-Δ5-steroid isomeraseIsomerase[Y16, Y32, Y57], [C81]
1PIP PapainPeptide hydrolysis (Cys protease)[C25, H159], [K17, K174, Y186], [R59], [R96]
1PSO PepsinPeptide hydrolysis (acid protease)[D32, D215, D303], [D11]
1WBA Winged bean albuminStorage–no known chemistryNo positive results
  • Positive results that form a cluster in coordinate space are shown in brackets. Active-site residues are shown in boldface. Second-shell residues are shown in italics. 

  • * Both 1AMQ and 1HKA are known to undergo conformational changes when the substrate binds. Calculations for both were run on the open (unbound) form. We note that the method still identifies the active site. K258 of 1AMQ is the residue that binds the cofactor. The calculation was run in the absence of cofactor.