One lineage, side by side
Every structure here was aligned onto IsPETase 6EQE when it was written, so these panels are already in register: rotating one rotates all of them, and the same view means the same orientation in every panel. The catalytic triad is drawn in yellow and substituted residues in pink, using the residues the geometry stage measured rather than positions inferred from an alignment.
The question this asks, which the catalogue cannot: do stabilising mutations keep clear of the catalytic machinery, or do some crowd it? Every substituted residue carries its side-chain distance to the nearest triad side chain, measured once from these coordinates. The wild types group asks a different question with the same machinery: those are natural enzymes from unrelated organisms that nobody has engineered, so what varies between them is what evolution did rather than what a protein engineer did.
Structures with no assigned lineage · 181–192 of 534
PAZy:21
crystal structure 7QJR, 1.51 Å · cleft 17.0 Å
PAZy:210
AlphaFold model
no triad measurable — this deposit is a catalytically inactivated form, with the nucleophilic serine replaced by alanine so the enzyme could be crystallised with substrate bound. The fold and every engineered substitution are right; the catalytic residue is simply not in the model, so the panel shows the whole molecule.
PAZy:211
ESMFold prediction, pLDDT 94 · cleft 22.7 Å
PAZy:213
AlphaFold model · cleft 24.5 Å
PAZy:214
ESMFold prediction, pLDDT 95 · cleft 24.7 Å
PAZy:215
crystal structure 7YM9, 1.34 Å · cleft 18.0 Å
PAZy:216-nonPET
ESMFold prediction, pLDDT 92 · cleft 22.8 Å
PAZy:22
AlphaFold model · cleft 17.0 Å
PAZy:223
AlphaFold model · cleft 26.1 Å
PAZy:224
ESMFold prediction, pLDDT 94 · cleft 22.0 Å
PAZy:225
AlphaFold model · cleft 26.4 Å
PAZy:226
ESMFold prediction, pLDDT 88 · cleft 25.5 Å
PAZy:210 has no measurable triad, and the reason is the deposit rather than the enzyme: these are inactivated crystallisation constructs with the catalytic serine mutated to alanine. Everything else about them is correct, including every engineered substitution, and the sequence held here is the active enzyme — only the coordinates are the knockout.
Distances are side chain to side chain, excluding backbone atoms. Measured any-atom to any-atom they came out at 1.31–1.35 Å for four variants, which is a peptide bond rather than a contact: those residues simply sit next to a triad residue in sequence. Where a substituted residue is adjacent in sequence it is marked, so a short distance that only reflects the fold's connectivity is visible as such. Panels built from predictions carry the loops that gate the cleft at lower confidence than the crystal structures beside them; a distance measured on one is weaker evidence than the same distance measured on the other.
Sequences one per panel above, in the same order
catalytic triad substitution against the lineage wild type · triad positions are labelled; hover any residue for its number. Click one to select it in its panel above, or click a residue in a panel to find it here.